Tm leveling compositions

ABSTRACT

Modified oligonucleotides are provided containing bases selected from unsubstituted and 3-substituted pyrazolo[3,4-d]pyrimidines and 5-substituted pyrimidines, and optionally have attached minor groove binders and reporter groups.

CROSS-REFERENCES TO RELATED APPLICATIONS

This application is a continuation of U.S. application Ser. No.09/796,988, filed Feb. 28, 2001, now U.S. Pat. No. 7,045,610 whichapplication claims the benefit of provisional application Ser. No.60/186,046, filed Mar. 1, 2000; and is a continuation-in-part of U.S.application Ser. No. 09/724,959, filed Nov. 28, 2000; now U.S. Pat. No.6,949,367 and is a continuation-in-part of U.S. application Ser. No.09/640,953, filed Aug. 16, 2000, now U.S. Pat. No. 6,492,346; which is acontinuation of U.S. application Ser. No. 09/054,832, filed Apr. 3,1998, now U.S. Pat. No. 6,312.894; and is a continuation-in-part of U.S.application Ser. No. 09/431,385, filed Nov. 1, 1999, now U.S. Pat. No.6,485,906; which is a continuation of U.S. application Ser. No.09/054,830, filed Apr. 3, 1998, now U.S. Pat. No. 6,127,121; thedisclosures of each being incorporated herein by reference.

STATEMENT AS TO RIGHTS TO INVENTIONS MADE UNDER FEDERALLY SPONSOREDRESEARCH AND DEVELOPMENT

Not applicable.

BACKGROUND OF THE INVENTION

This application is in the field of molecular biology relating to theuse of oligonucleotides as probes and primers in liquid, solid and mixedphase assays. The application further relates to the use of modifiednucleic acid bases and modified oligonucleotides to improve thehybridization properties and discriminatory abilities ofoligonucleotides that are used in arrays and as probes and primers.

Many techniques currently in use in molecular biology utilizeoligonucleotides as probes and/or primers. It is often advantageous, inthe practice of these techniques, to be able to distinguish between twoor more sequences which are related but which differ by one or morenucleotides. For example, many mutations of clinical significance differby only a single nucleotide from the wild-type sequence. Polymorphismsin mammalian genomes are also often characterized by sequencedifferences of one or a few nucleotides. The ability to make such adistinction is known as mismatch discrimination. In practical terms,mismatch discrimination describes the property by which a definedsequence oligonucleotide, at a given stringency, hybridizes strongly(one manifestation of which is that the hybrids have a high meltingtemperature) to a target sequence with which it is complementary alongits entire length (a perfect hybrid or perfect match), but hybridizesdetectably more weakly to a target sequence that is non-complementary tothe sequence of the oligonucleotide at one or a few nucleotides (amismatch). The differences in hybridization strength are such that aparticular stringency can be selected at which a perfect match isdetectable as a hybrid and a mismatch fails to form a hybrid.

In a nucleic acid duplex, each base pair contributes to stability.Hence, the shorter the duplex, the greater the relative contribution ofeach individual base pair to the stability of the duplex. As a result,the difference in stability between a perfect match and a mismatch willbe greater for shorter oligonucleotides. However, short oligonucleotideshybridize weakly, even to a perfectly complementary sequence, and thusmust be hybridized under conditions of reduced stringency. Thus, thepotential discriminatory power of short oligonucleotides cannot beeasily realized except under conditions of low stringency.

What is needed in the art are new methods for mismatch discrimination,particularly for single-nucleotide mismatches, under conditions of highstringency; for example, at the elevated temperatures characteristic ofmost nucleic acid amplification reactions. Surprisingly, the presentinvention provides such methods, along with new reagents andcompositions which can be used in the methods.

SUMMARY OF THE INVENTION

The present invention provides a number of modified oligonucleotidesfound to have exceptional properties and usefulness in a variety ofassays. Accordingly, the present invention also provides methods forusing the modified oligonucleotides described herein.

In one aspect, the present invention provides modified oligonucleotideshaving at least two bases selected from unsubstituted and 3-substitutedpyrazolo[3,4-d]pyrimidine bases. In preferred embodiments, theoligonucleotides having modified bases will further comprise othermoieties such as detectable labels, fluorescence and chemiluminescencequenchers and/or minor groove binders and/or other types of modifiedbases or base analogs.

In another aspect, the present invention provides modifiedoligonucleotides having at least one 5-substituted pyrimidine base andat least one 3-substituted pyrazolo[3,4-d]pyrimidine base. In preferredembodiments, these modified oligonucleotides will further comprise othermoieties (as above) such as detectable labels, fluorescence andchemiluminescence quenchers and/or minor groove binders.

In yet another aspect, the present invention provides methods fordistinguishing polynucleotides having related sequences.

In still another aspect, the present invention provides methods fordetecting the presence of a target sequence in a polynucleotide.

In still other aspects, the present invention provides methods forprimer extension, and methods for determining the nucleotide sequence ofa polynucleotide.

In related aspects, the present invention provides methods for examininggene expression in a cell, and methods for identifying a mutation orpolymorphism in a target sequence of a gene of interest.

In still another aspect, the present invention provides a number ofmodified bases that are useful in preparing modified oligonucleotidesfor the methods described herein and other conventional assays andmethods.

In yet another aspect, the present invention provides modifiedoligonucleotide arrays wherein the array members have T_(m)s withinabout 1-2° C. and lengths within 1-2 bases from each other. Methods arealso provided for determining sequences of the array members.

BRIEF DESCRIPTION OF THE DRAWINGS

FIGS. 1A and 1B provide structures for several modified bases and theirabbreviations. The wavy line is used to denote the position of anattached sugar moiety (unprotected, protected, activated and the like).

FIG. 2 is a graph illustrating the balancing of the T_(m) of 8-merGC-rich and AT-rich probes with different combinations of MGB, PPPA andPU.

FIG. 3 is a chart which illustrates one advantage achieved through theuse of PPPA and PPG in MGB-modified oligonucleotide probes. As seen inthe figure, the modified bases allow shortening of the probe that showsincreased mismatch discrimination in real-time PCR. Ã is PPPA and {hacekover (G)} is PPG. MGB-modified FAM probe=SEQ ID NO: 1; MGB-modified FAMprobe complement=SEQ ID NO: 2; PPPA and PPG containing MGB-modified FAMprobe complement=SEQ ID NO: 3; PPPA and PPG containing MGB-modified FAMprobe=SEQ ID NO: 4.

FIG. 4 illustrates an Invader™ assay in which the modifiedoligonucleotides of the invention can be used.

FIG. 5 illustrates a comparison of Invader™ probe performance withdifferent numbers of PPGs (SEQ ID NOS:5-7).

DESCRIPTION OF THE INVENTION

Abbreviations and Definitions

Abbreviations for a number of the modified bases described herein areprovided as follows (structures of these bases are shown in FIGS. 1A and1B): 6-amino-3-prop-1-ynyl-5-hydropyrazolo[3,4-d]pyrimidine-4-one, PPPG;6-amino-3-(3-hydroxyprop-1-yny)1-5-hydropyrazolo[3,4-d]pyrimidine-4-one,HOPPPG;6-amino-3-(3-aminoprop-1-ynyl)-5-hydropyrazolo[3,4-d]pyrimidine-4-one,NH₂PPPG; 4-amino-3-(prop-1-ynyl)pyrazolo[3,4-d]pyrimidine, PPPA;4-amino-3-(3-hydroxyprop-1-ynyl)pyrazolo[3,4-d]pyrimidine, HOPPPA;4-amino-3-(3-aminoprop-1-ynyl)pyrazolo[3,4-d]pyrimidine, NH₂PPPA;3-prop-1-ynylpyrrazolo [3,4-d]pyrimidine-4,6-diamino, (NH₂)₂PPPA;2-(4,6-diaminopyrazolo[3,4-d]pyrimidin-3-yl)ethyn-1-ol, (NH₂)₂PPPAOH;3-(2-aminoethynyl)pyrazolo[3,4-d]pyrimidine-4,6-diamine, (NH₂)₂PPPANH₂;5-prop-1-ynyl-1,3-dihydropyrimidine-2,4-dione, PU;5-(3-hydroxyprop-1-ynyl)-1,3-dihydropyrimidine-2,4-dione, HOPU;6-amino-5-prop-1-ynyl-3-dihydropyrimidine-2-one, PC;6-amino-5-(3-hydroxyprop-1-yny)-1,3-dihydropyrimidine-2-one, HOPC; and6-amino-5-(3-aminoprop-1-yny)-1,3-dihydropyrimidine-2-one, NH₂PC;5-[4-amino-3-(3-methoxyprop-1-ynyl)pyrazol[3,4-d]pyrimidinyl]-2-(hydroxymethyl)oxolan-3-ol, CH₃OPPPA;6-amino-1-[4-hydroxy-5-(hydroxymethyl)oxolan2-yl]-3-(3-methoxyprop-1-ynyl)-5-hydropyrazolo[3,4-d]pyrimidin-4-one,CH₃OPPPG; 5-(4-hydroxybut-1-ynyl)-1,3-dihydropyrimidine-2,4-dione,HOBuU; 6-amino-5-(4-hydroxybut-1-ynyl)-3-hydropyrimidine-2-one, HOBuC;4-(4-aminopyrazolo[3,4-d]pyrimidin-3-yl)but-3-yn-1-ol, HOBuPPA;6-amino-3-(4-hydroxybut-1-ynyl)pyrazolo[3,4-d]pyrimidin-4-ol, HOBuPPG;4-(4,6-diaminopyrazolo[3,4-d]pyrimidin-3-yl)but-3-yn-1-ol,(NH₂)₂BuPPAOH.

Unless otherwise stated, the following terms used in the specificationand claims have the meanings given below:

The term “alkyl” refers to a linear, branched, or cyclic saturatedmonovalent hydrocarbon radical or a combination of cyclic and linear orbranched saturated monovalent hydrocarbon radicals having the number ofcarbon atoms indicated in the prefix. For example, (C₁-C₈)alkyl is meantto include methyl, ethyl, n-propyl, 2-propyl, tert-butyl, pentyl,cyclopentyl, cyclopropylmethyl and the like. For each of the definitionsherein (e.g., alkyl, alkenyl, alkoxy, aralkyloxy), when a prefix is notincluded to indicate the number of main chain carbon atoms in an alkylportion, the radical or portion thereof will have eight or fewer mainchain carbon atoms.

The term “alkylene” means a linear saturated divalent hydrocarbonradical or a branched saturated divalent hydrocarbon radical having thenumber of carbon atoms indicated in the prefix. For example,(C₁-C₆)alkylene is meant to include methylene, ethylene, propylene,2-methylpropylene, pentylene, and the like.

The term “alkenyl” refers to a linear monovalent hydrocarbon radical ora branched monovalent hydrocarbon radical having the number of carbonatoms indicated in the prefix and containing at least one double bond.For example, (C₂-C₆)alkenyl is meant to include, ethenyl, propenyl, andthe like.

The term “alkynyl” refers to a linear monovalent hydrocarbon radical ora branched monovalent hydrocarbon radical containing at least one triplebond and having the number of carbon atoms indicated in the prefix. Forexample, (C₂-C₆)alkynyl is meant to include ethynyl, propynyl, and thelike.

The terms “alkoxy,” “alkylamino” and “alkylthio” (or thioalkoxy) areused in their conventional sense, and refer to those alkyl groupsattached to the remainder of the molecule via an oxygen atom, an aminogroup, or a sulfur atom, respectively. Similarly, the term dialkylaminorefers to an amino group having two attached alkyl groups that can bethe same or different.

The term “aryl” means a monovalent monocyclic or bicyclic aromatichydrocarbon radical of 6 to 10 ring atoms which is unsubstituted orsubstituted independently with one to four substituents, preferably one,two, or three substituents selected from alkyl, cycloalkyl,cycloalkyl-alkyl, halo, nitro, cyano, hydroxy, alkoxy, amino, acylamino,mono-alkylamino, di-alkylamino, haloalkyl, haloalkoxy, heteroalkyl, COR(where R is hydrogen, alkyl, cycloalkyl, cycloalkyl-alkyl, phenyl orphenylalkyl), —(CR′R″)_(n)—COOR (where n is an integer from 0 to 5, R′and R″ are independently hydrogen or alkyl, and R is hydrogen, alkyl,cycloalkyl, cycloalkylalkyl, phenyl or phenylalkyl) or—(CR′R″)_(n)—CONR^(a)R^(b) (where n is an integer from 0 to 5, R′ and R″are independently hydrogen or alkyl, and R^(a) and R^(b) are,independently of each other, hydrogen, alkyl, cycloalkyl,cycloalkylalkyl, phenyl or phenylalkyl). More specifically the term arylincludes, but is not limited to, phenyl, biphenyl, 1-naphthyl, and2-naphthyl, and the substituted forms thereof. Similarly, the term“heteroaryl” refers to those aryl groups wherein one or more heteroatomsor heteroatom functional groups have replaced a ring carbon, whileretaining aromatic properties, e.g., pyridyl, quinolinyl, quinazolinyl,thienyl, and the like. For brevity, the term aryl, when used incombination with other radicals (e.g., aryloxy, arylalkyl) is meant toinclude both aryl groups and heteroaryl groups as described above.

The term “arylalkyl” refers to a radical —R^(a)R^(b) where R^(a) is analkylene group (having the indicated number of carbon atoms, or ifunspecified having six or fewer main chain carbon atoms) and R^(b) is anaryl group as defined herein. Examples of arylalkyl groups includebenzyl, phenylethyl, 3-(3-chlorophenyl)-2-methylpentyl, and the like.

Similarly the term “arylalkenyl” means a radical —R^(a)R^(b) where R^(a)is an alkenylene group and R^(b) is an aryl group as defined herein,e.g., 3-phenyl-2-propenyl, and the like.

“Arylheteroalkyl” means a radical —R^(a)R^(b) where R^(a) is anheteroalkylene group (having the indicated number of carbon atoms) andR^(b) is an aryl group as defined herein, e.g.,2-hydroxy-2-phenyl-ethyl, 2-hydroxy-1-hydroxymethyl-2-phenyl-ethyl, andthe like.

The term “aryloxy”, refers to a radical —OR where R is an aryl group,e.g., phenoxy, naphthyloxy and the like.

The prefix “halo” and the term “halogen” when used to describe asubstituent, refer to —F, —Cl, —Br and —I.

The term “heteroalkyl” refers to an alkyl radical as defined herein withone, two or three substituents independently selected from cyano,—OR^(a), —NR^(b)R^(c), and —S(O)_(n)R^(d) (where n is an integer from 0to 2), with the understanding that the point of attachment of theheteroalkyl radical is through a carbon atom of the heteroalkyl radical.R^(a) is hydrogen, alkyl, aryl, arylalkyl, alkoxycarbonyl,aryloxycarbonyl, carboxamido, or mono- or di-alkylcarbamoyl. R^(b) ishydrogen, alkyl, aryl or arylalkyl. R^(c) is hydrogen, alkyl, aryl,arylalkyl, alkoxycarbonyl, aryloxycarbonyl, carboxamido, mono- ordi-alkylcarbamoyl or alkylsulfonyl, R^(d) is hydrogen (provided that nis 0), alkyl, aryl, arylalkyl, amino, mono-alkylamino, di-alkylamino, orhydroxyalkyl. Representative examples include, for example,2-hydroxyethyl, 2,3-dihydroxypropyl, 2-methoxyethyl, benzyloxymethyl,2-cyanoethyl, and 2-methylsulfonyl-ethyl. For each of the above, R^(a),R^(b),R^(c), and R^(d) can be further substituted by NH₂, fluorine,alkylamino di-alkylamino, OH or alkoxy. Additionally, the prefixindicating the number of carbon atoms (e.g., C₁-C₁₀) refers to the totalnumber of carbon atoms in the portion of the heteroalkyl group exclusiveof the cyano, —OR^(a), —NR^(b)R^(c), or —S(O)_(n)R^(d) portions.

The term “heterocyclyl” refers to a saturated or unsaturatednon-aromatic cyclic radical of 3 to 8 ring atoms in which one or tworing atoms are heteroatoms selected from O, NR (where R is independentlyhydrogen or alkyl) or S(O)_(n) (where n is an integer from 0 to 2), theremaining ring atoms being C, where one or two C atoms may optionally bereplaced by a carbonyl group. The heterocyclyl ring may be optionallysubstituted independently with one, two, or three substituents selectedfrom alkyl, halo, nitro, cyano, hydroxy, alkoxy, amino, mono-alkylamino,di-alkylamino, haloalkyl, haloalkoxy, —COR (where R is hydrogen, alkyl,cycloalkyl, cycloalkyl-alkyl, phenyl or phenylalkyl), —(CR′R″)_(n)—COOR(n is an integer from 0 to 5, R′ and R″ are independently hydrogen oralkyl, and R is hydrogen, alkyl, cycloalkyl, cycloalkyl-alkyl, phenyl orphenylalkyl), or —(CR′R″)_(n)—CONR^(a)R^(b) (where n is an integer from0 to 5, R′ and R″ are independently hydrogen or alkyl, and R^(a) andR^(b) are, independently of each other, hydrogen, alkyl, phenyl orphenylalkyl). More specifically the term heterocyclyl includes, but isnot limited to, tetrahydropyranyl, piperidino, N-methylpiperidin-3-yl,piperazino, N-methylpyrrolidin-3-yl, 3-pyrrolidino, 2-pyrrolidon-1-yl,morpholino, thiomorpholino, thiomorpholino-1-oxide,thiomorpholino-1,1-dioxide, pyrrolidinyl, and the derivatives thereof.The prefix indicating the number of carbon atoms (e.g., C₃-C₁₀) refersto the total number of carbon atoms in the portion of the heterocyclylgroup exclusive of the number of heteroatoms.

The terms “heterocyclylalkyl,” “heterocyclylalkenyl,”“heterocyclylalkynyl” refer to radicals —R^(a)R^(b) where R^(a) is analkylene, alkenylene or alkynylene group, respectively, and R^(b) is aheterocyclyl group as defined herein, e.g., tetrahydropyran-2-ylmethyl,4-methylpiperazin-1-ylethyl, 3-piperidinylmethyl, and the like.

The terms “heteroalkylene” means a linear saturated divalent hydrocarbonradical of one to six carbons or a branched saturated hydrocarbonradical of three to six carbon atoms with one, two or three substituentsindependently selected from —OR^(a), —NR^(b)R^(c), and —S(O)_(n)R^(d)(where n is an integer from 0 to 2) where, R^(a), Rb, Rc, and R^(d) areas defined herein for a heteroalkyl radical. Examples include,2-hydroxyethan-1,2-diyl, 2-hydroxypropan-1,3-diyl and the like.

Each of the above terms (e.g., “alkyl,” “heteroalkyl,” and “aryl”) aremeant to include both substituted and unsubstituted forms of theindicated radical. Preferred substituents for each type of radical areprovided below.

Substituents for the alkyl and heteroalkyl radicals (including thosegroups often referred to as alkylene, alkenyl, heteroalkylene,heteroalkenyl, alkynyl, heterocycloalkyl, and heterocycloalkenyl) can bea variety of groups selected from: —OR′, ═O, ═NR′, ═N—OR′, —NR′R″, —SR′,-halogen, —SiR′R″R′″, —OC(O)R′, —C(O)R′, —CO₂R′, —CONR′R″, —OC(O)NR′R″,—NR″C(O)R′, —NR′—C(O)NR″R′″, —NR″C(O)₂R′, —NH—C(NH₂)═NH, —NR′C(NH₂)═NH,—NH—C(NH₂)═NR′, —S(O)R′, —S(O)₂R′, —S(O)₂NR′R″, —CN and —NO₂ in a numberranging from zero to four, preferably, zero, one, two or threesubstituents. R′, R″ and R′″ each independently refer to hydrogen,unsubstituted (C₁-C₈)alkyl and heteroalkyl, unsubstituted aryl, arylsubstituted with 1-3 halogens, unsubstituted alkyl, alkoxy or thioalkoxygroups, or aryl-(C₁-C₄)alkyl groups. When R′ and R″ are attached to thesame nitrogen atom, they can be combined with the nitrogen atom to forma 5-, 6-, or 7-membered ring. For example, —NR′R″ is meant to include1-pyrrolidinyl and 4-morpholinyl. From the above discussion ofsubstituents, one of skill in the art will understand that the term“alkyl” in its broadest sense is meant to include groups such ashaloalkyl (e.g., —CF₃ and —CH₂CF₃) and acyl (e.g., —C(O)CH₃, —C(O)CF₃,—C(O)CH₂OCH₃, and the like). Preferably, the alkyl groups will have from0-3 substituents, more preferably 0, 1, or 2 substituents, unlessotherwise specified.

Similarly, substituents for the aryl groups are varied and are selectedfrom: -halogen, —OR′, —OC(O)R′, —NR′R″, —SR′, —R′, —CN, —NO₂, —CO₂R′,—CONR′R″, —C(O) R′, —OC(O)NR′R″, —NR″C(O)R′, —NR″C(O)₂R′,—NR′—C(O)NR″R′″, —NH—C(NH₂)═NH, —NR′C(NH₂)═NH, —NH—C(NH₂)═NR′, —S(O)R′,—S(O)₂R′, —S(O)₂NR′R″, —N₃, —CH(Ph)₂, perfluoro(C₁-C₄)alkoxy, andperfluoro(C₁-C₄)alkyl, in a number ranging from zero to the total numberof open valences on the aromatic ring system; and where R′, R″ and R′″are independently selected from hydrogen, (C₁-C₈)alkyl and heteroalkyl,unsubstituted aryl and heteroaryl, (unsubstituted aryl)-(C₁-C₄)alkyl,and (unsubstituted aryl)oxy-(C₁-C₄)alkyl.

Two of the substituents on adjacent atoms of the aryl or heteroaryl ringmay optionally be replaced with a substituent of the formula-T-C(O)—(CH₂)_(q)—U—, wherein T and U are independently —NH—, —O—, —CH₂—or a single bond, and q is an integer of from 0 to 2. Alternatively, twoof the substituents on adjacent atoms of the aryl or heteroaryl ring mayoptionally be replaced with a substituent of the formula-A-(CH₂)_(r)—B—, wherein A and B are independently —CH₂—, —O—, —NH—,—S—, —S(O)—, —S(O)₂—, —S(O)₂NR′— or a single bond, and r is an integerof from 1 to 3. One of the single bonds of the new ring so formed mayoptionally be replaced with a double bond. Alternatively, two of thesubstituents on adjacent atoms of the aryl or heteroaryl ring mayoptionally be replaced with a substituent of the formula—(CH₂)_(s)—X—(CH₂)_(t)—, where s and t are independently integers offrom 0 to 3, and X is —O—, —NR′—, —S—, —S(O)—, —S(O)₂—, or —S(O)₂NR′—.The substituent R¹ in —NR′— and —S(O)₂NR′— is selected from hydrogen orunsubstituted (C₁-C₆)alkyl.

Certain compounds or oligonucleotides of the present invention may existin a salt form. Such salts include base addition salts such as sodium,potassium, calcium, ammonium, organic amino, or magnesium salt, or asimilar salt. When the compounds or modified oligonucleotides of thepresent invention contain relatively basic functionalities, acidaddition salts can be obtained by contacting the neutral form of suchcompounds with a sufficient amount of the desired acid, either neat orin a suitable inert solvent. Examples of acceptable acid addition saltsinclude those derived from inorganic acids like hydrochloric,hydrobromic, nitric, carbonic, monohydrogencarbonic, phosphoric,monohydrogenphosphoric, dihydrogenphosphoric, sulfuric,monohydrogensulfuric, hydriodic, or phosphorous acids and the like, aswell as the salts derived from organic acids like acetic, propionic,isobutyric, maleic, malonic, lactic, benzoic, succinic, suberic,fumaric, mandelic, phthalic, benzenesulfonic, p-tolylsulfonic, citric,tartaric, methanesulfonic, and the like. Also included are salts ofamino acids such as arginate and the like, and salts of organic acidslike glucuronic or galactunoric acids and the like (see, for example,Berge, S. M., et al, “Pharmaceutical Salts”, Journal of PharmaceuticalScience, 1977, 66, 1-19). Certain specific compounds of the presentinvention contain both basic and acidic functionalities that allow thecompounds to be converted into either base or acid addition salts.

The neutral forms of the compounds may be regenerated by contacting thesalt with a base or acid and isolating the parent compound in theconventional manner. The parent form of the compound differs from thevarious salt forms in certain physical properties, such as solubility inpolar solvents, but otherwise the salts are equivalent to the parentform of the compound for the purposes of the present invention.

Certain compounds of the present invention can exist in unsolvated formsas well as solvated forms, including hydrated forms. In general, thesolvated forms are equivalent to unsolvated forms and are intended to beencompassed within the scope of the present invention. Certain compoundsof the present invention may exist in multiple crystalline or amorphousforms. In general, all physical forms are equivalent for the usescontemplated by the present invention and are intended to be within thescope of the present invention.

Certain compounds of the present invention possess asymmetric carbonatoms (optical centers) or double bonds; the racemates, diastereomers,geometric isomers and individual isomers are all intended to beencompassed within the scope of the present invention. The methods forthe determination of stereochemistry and the separation of isomers arewell-known in the art (see discussion in Chapter 4 of “Advanced OrganicChemistry”, 4th edition J. March, John Wiley and Sons, New York, 1992).

The compounds of the present invention may also contain unnaturalproportions of atomic isotopes at one or more of the atoms thatconstitute such compounds. For example, the compounds may beradiolabeled with radioactive isotopes, such as for example tritium(³H), iodine-125 (¹²⁵I) or carbon-14 (¹⁴C). All isotopic variations ofthe compounds of the present invention, whether radioactive or not (e.g,²H), are intended to be encompassed within the scope of the presentinvention.

“Protecting group” or “protected form thereof” refers to a grouping ofatoms that when attached to a reactive group in a molecule masks,reduces or prevents that reactivity. Examples of protecting groups canbe found in T. W. Greene and P. G. Futs, Protective Groups in OrganicChemistry, (Wiley, 2nd ed. 1991), Beaucage and Iyer, Tetrahedron48:2223-2311 (1992), and Harrison and Harrison et al., Compendium ofSynthetic Organic Methods, Vols. 1-8 (John Wiley and Sons. 1971-1996).Representative amino protecting groups include formyl, acetyl,trifluoroacetyl, benzyl, benzyloxycarbonyl (CBZ), tert-butoxycarbonyl(Boc), trimethyl silyl (TMS), 2-trimethylsilyl-ethanesulfonyl (SES),trityl and substituted trityl groups, allyloxycarbonyl,9-fluorenylmethyloxycarbonyl (FMOC), nitro-veratryloxycarbonyl (NVOC)and the like. Representative hydroxy protecting groups include thosewhere the hydroxy group is either acylated or alkylated such as benzyland trityl ethers as well as alkyl ethers, tetrahydropyranyl ethers,trialkylsilyl ethers and allyl ethers.

“Optional” or “optionally” in the above definitions means that thesubsequently described event or circumstance may but need not occur, andthat the description includes instances where the event or circumstanceoccurs and instances in which it does not. For example, “heterocyclogroup optionally mono- or di- substituted with an alkyl group” meansthat the alkyl may but need not be present, and the description includessituations where the heterocyclo group is mono- or disubstituted with analkyl group and situations where the heterocyclo group is notsubstituted with the alkyl group.

The practice of the present invention will employ, unless otherwiseindicated, conventional techniques in organic chemistry, biochemistry,oligonucleotide synthesis and modification, bioconjugate chemistry,nucleic acid hybridization, molecular biology, microbiology, genetics,recombinant DNA, and related fields as are within the skill of the art.These techniques are fully explained in the literature. See, forexample, Maniatis, Fritsch & Sambrook, MOLECULAR CLONING: A LABORATORYMANUAL, Cold Spring Harbor Laboratory Press (1982); Sambrook, Fritsch &Maniatis, MOLECULAR CLONING: A LABORATORY MANUAL, Second Edition, ColdSpring Harbor Laboratory Press (1989); Ausubel, et al., CURRENTPROTOCOLS IN MOLECULAR BIOLOGY, John Wiley & Sons (1987, 1988, 1989,1990, 1991, 1992, 1993, 1994, 1995, 1996); Gait (ed.), OLIGONUCLEOTIDESYNTHESIS: A PRACTICAL APPROACH, IRL Press (1984); Eckstein (ed.),OLIGONUCLEOTIDES AND ANALOGUES: A PRACTICAL APPROACH, IRL Press (1991).

General

Oligonucleotides are short polymers of nucleotides, generally less than200 nucleotides, preferably less than 150 nucleotides, more preferablyless than 100 nucleotides, more preferably less than 50 nucleotides andmost preferably less than 21 nucleotides in length. Polynucleotides aregenerally considered, in the art, to comprise longer polymers ofnucleotides than do oligonucleotides, although there is anart-recognized overlap between the upper limit of oligonucleotide lengthand the lower limit of polynucleotide length. With respect to thepresent invention, “oligonucleotide” generally refers to a nucleic acid,usually comprising a detectable label, that is used as a probe or as aprimer; while polynucleotide refers to a nucleic acid containing atarget sequence. Consequently, for the purposes of the presentinvention, the terms “oligonucleotide” and “polynucleotide” shall not beconsidered limiting with respect to polymer length.

The present invention provides modified oligonucleotides having new andsurprising properties of superior mismatch discrimination, compared tounmodified oligonucleotides. Modified oligonucleotides of the inventionare used as probes, wherein their hybridization to a target sequence isdetected, or as primers, wherein their hybridization to a targetsequence is followed by polynucleotide synthesis initiated from the 3′terminus of the modified oligonucleotide, and the synthesized product(i.e., the extension product) is detected.

A target sequence refers to a nucleotide sequence which comprises a siteof hybridization for a probe or a primer. Target sequences can be foundin any nucleic acid including, but not limited to, genomic DNA, cDNA,RNA and any amplified product thereof, and can comprise a wild-type genesequence, a mutant gene sequence, a non-coding sequence, a regulatorysequence, etc. A target sequence will generally be less than 100nucleotides, preferably less than 50 nucleotides, and most preferably,less than 21 nucleotides in length.

DESCRIPTION OF THE EMBODIMENTS

The present invention provides a number of modified oligonucleotideswhich can generally be divided into three groups.

The first group of modified oligonucleotides are those having at leasttwo modified bases replacing the naturally-occurring bases. Here, themodified bases will be unsubstituted or 3-substitutedpyrazolo[3,4-d]pyrimidines. In some embodiments, however, the modifiedbases will be selected such that at least one of the bases is a5-substituted pyrimidine and at least one of the bases is anunsubstituted or a 3-substituted pyrazolo[3,4-d]pyrimidine. Preferably,this group of modified oligonucleotides will have additional attachedgroups (e.g., minor groove binders, reporter groups, quenchers, etc.)which assist during assays to detect target sequences.

The second group of modified oligonucleotides are those having at leastone modified base, but also having an attached minor groove binder,reporter group, quencher, or the like.

The third group of modified oligonucleotides are those that comprise oneor more of the novel modified bases described below. As in the firstgroup, this group of modified oligonucleotides will preferably haveattached groups selected from, for example, minor groove binders,reporter groups or quenchers.

Modified Oligonucleotides

In one aspect, the present invention provides modified oligonucleotidescomprising at least two bases selected from the group consisting ofunsubstituted and 3-substituted pyrazolo[3,4-d]pyrimidine bases.

The pyrazolo[3,4-d]pyrimidine bases are those bases in which a pyrazolering is fused to a pyrimidine ring in the following specificorientation:

in which the wavy line indicates the point of attachment between thebase and either an attached oligomer-forming sugar or an amino acidinvolved in peptide nucleic acid formation. Additionally, the groups X¹and X² are independently H, OH or NH₂ such that thepyrazolo[3,4-d]pyrimidine bases approximate the construction of thenatural purine bases, guanosine, adenine and inosine, as well as relatedderivatives of those bases. In this group of embodiments, an“unsubstituted pyrazolo[3,4-d]pyrimidine base” refers to those bases ofthe general formula Ia, while the term “3-substitutedpyrazolo[3,4-d]pyrimidine base” refers to those bases having the formulaIb, in which R¹ is defined as described below.

In formula Ib, the symbols X¹ and X² independently represent H, OH, NH₂or a protected form thereof. The symbol R¹ represents a member selectedfrom (C₁-C₁₂)heteroalkyl, (C₂-C₁₂)heteroalkenyl, (C₂-C₁₂)heteroalkynyl,—O—(C₁-C₁₂)alkyl, —O—(C₁-C₁₂) alkyl, —O—(C₂-C₁₂)alkenyl,—O—(C₂-C₁₂)alkynyl, —S—(C₁-C₁₂)alkyl, —S—(C₂-C₁₂)alkenyl, —S—(C₂-C₁₂alkynyl, heterocyclyl(C₁-C₁₂)alkyl, heterocyclyl(C₂-C₁₂)alkenyl,heterocyclyl(C₂-C₁₂)alkynyl, aryl(C₁-C₁₂) alkyl, aryl(C₂-C₁₂)alkenyl,aryl(C₂-C₁₂)alkynyl, aryl, heterocyclyl, halogen, —CN, —CONH₂ andprotected forms thereof. Preferred heteroalkyl, heteroalkenyl andheteroalkynyl groups are those that terminate (distal to thepyrazolo[3,4-d]pyrimidine ring system) in a heteroatom group (e.g., OH,NH₂, SH and the like). For example, preferred heteroalkyl, heteroalkenyland heteroalkynyl groups include 3-amino-1-propyl, 4-hydroxy-1-butyl,3-amino-1-propyn-1-yl, 3-hydroxy-1-propyn-1-yl,4-hydroxy-3-hydroxymethyl-1-butyn-1-yl, 4-hydroxy-1-butyn-1-yl, andtheir higher homologs. Other preferred R¹ groups include those whichterminate in an aryl or heterocyclic group (e.g.,heterocyclyl(C₁-C₁₂)alkyl, heterocyclyl(C₂-C₂)alkenyl,heterocyclyl(C₂-C₁₂)alkynyl, aryl(C₁-C₁₂)alkyl, aryl(C₂-C₁₂)alkenyl andaryl(C₂-C₁₂)alkynyl). Preferred aryl and heterocyclic groups are eithersubstituted or unsubstituted phenyl, thienyl, thiazolyl, imidazolyl,furanyl, oxazolyl, pyridinyl, pyrrolyl, indolyl, benzimidazolyl,benzthiazolyl and benzoxazolyl.

In particularly preferred embodiments, the pyrazolo[3,4-d]pyrimidinebase is selected from:

Still more preferably, the modified bases are selected from Ic, Id or Iewherein each R¹ is a propynyl, hydroxypropynyl, aminopropynyl,aminobutynyl, hydroxybutynyl, or a substituted or unsubstituted phenyl,thienyl, thiazolyl, imidazolyl, furanyl, oxazolyl, pyridinyl, pyrrolyl,indolyl, benzimidazolyl, benzthiazolyl or benzoxazolyl group attacheddirectly to the pyrazolo[3,4-d]pyrimidine ring system or attached to thering system via a one to four carbon linking group which can besaturated (e.g., ethylene, propylene, butylene) or unsaturated (e.g.,acetylenyl, propynylene, butynylene, propenylene, butenylene).

The modified oligonucleotides of the present invention have a backbonesuch as, for example, that found with the naturally-occurringoligonucleotides or peptide-nucleic acids (e.g., heterocyclic basesattached to oligomer-forming sugars or peptide-nucleic acid-formingamino acids). Alternative oligomeric backbones are known to those ofskill in the art (referred to below as “modified” backbones orcomprising backbone modifications). For the purpose of this invention amodified oligonucleotide is any oligomeric polymer, including thenatural phosphate backbone and non-natural backbones, that containsnatural and/or modified bases and retains the ability to hybridizespecifically to a complementary nucleic acid to form a stable duplex.

In preferred embodiments, the modified oligonucleotides of the inventionhave a backbone of sugar or glycosidic moieties, preferably2-deoxyribofuranosides wherein all internucleotide linkages are thenaturally occurring phosphodiester linkages. In alternative embodimentshowever, the 2-deoxy-β-D-ribofuranose groups are replaced with othersugars, for example, β-D-ribofuranose. In addition, β-D-ribofuranose maybe present wherein the 2—OH of the ribose moiety is alkylated with aC₁₋₆ alkyl group (2-(O—C₁₋₆ alkyl) ribose) or with a C₂₋₆ alkenyl group(2-(O—C₂₋₆ alkenyl) ribose), or is replaced by a fluoro group(2-fluororibose). Related oligomer-forming sugars useful in the presentinvention are those that are “locked”, i.e., contain a methylene bridgebetween C-4′ and an oxygen atom at C-2′. Other sugar moieties compatiblewith hybridization of the oligonucleotide can also be used, and areknown to those of skill in the art, including, but not limited to,α-D-arabinofuranosides, α-2′-deoxyribofuranosides or2′,3′-dideoxy-3′-aminoribofuranosides. Oligonucleotides containingα-D-arabinofuranosides can be prepared as described in U.S. Pat. No.5,177,196. Oligonucleotides containing2′,3′-dideoxy-3′-aminoribofuranosides are described in Chen et al.((1995) Nucleic Acids Res. 23:2661-2668). Synthetic procedures forlocked nucleic acids (Singh et al, Chem. Comm., 455-456 (1998); WengelJ., Acc. Chem. Res., 32:301-310 (1998)) and oligonucleotides containing2′-halogen-2′-deoxyribofuranosides (Palissa et al., Z. Chem. 27:216(1987)) have been described. The phosphate backbone of the modifiedoligonucleotides described herein can also be modified so that theoligonucleotides contain phosphorothioate linkages and/ormethylphosphonates and/or phosphoroamidates (Chen et al., Nucl. AcidsRes., 23:2662-2668 (1995)). Combinations of oligonucleotide linkages arealso within the scope of the present invention. Still other backbonemodifications are known to those of skill in the art.

In another group of embodiments, the modified bases described herein areincorporated into PNA and DNA/PNA chimeras to balance T_(m)s and providemodified oligonucleotides having improved mismatch discrimination.Various modified forms of DNA and DNA analogues have been used inattempts to overcome some of the disadvantages of the use of DNAmolecules as probes and primers. Among these are peptide nucleic acids(PNAs, also known as polyamide nucleic acids). Nielsen et al. (1991)Science 254:1497-1500. PNAs contain heterocyclic base units, as found inDNA and RNA, that are linked by a polyamide backbone, instead of thesugar-phosphate backbone characteristic of DNA and RNA. PNAs are capableof hybridization to complementary DNA and RNA target sequences and, infact, hybridize more strongly than a corresponding nucleic acid probe.The synthesis of PNA oligomers and reactive monomers used in thesynthesis of PNA oligomers have been described in U.S. Pat. Nos.5,539,082; 5,714,331; 5,773,571; 5,736,336 and 5,766,855. Alternateapproaches to PNA and DNA/PNA chimera synthesis and monomers for PNAsynthesis have been summarized. Uhlmann et al. (1998) Angew. Chem. Int.Ed. 37:2796-2823. Accordingly, the use of any combination of normalbases, unsubstituted pyrazolo[3,4-d]pyrimidine bases (e.g., PPG andPPA), 3-substituted pyrazolo[3,4-d]pyrimidines, modified purine,modified pyrimidine, 5-substituted pyrimidines, universal bases or aminor groove binder to balance the T_(m) of a PNA or DNA/PNA chimera isin the scope of this invention. A variety of universal bases are knownin the art. Other universal bases have recently been described and arealos useful in the present invention (see, Seela, et al., XIVInternational Round Table: Nucleosides, Nucleotides and Their BiologicalApplications, Sep. 10-14, 2000, San Francisco Calif., pp. 40). Thesynthetic methods necessary for the synthesis of modified base monomericunits required for PNA and PNA/DNA chimeras synthesis are available inthe art, see methods in this application and Uhlmann et al. Angew. Chem.Int. Ed. 37:2796-2823 (1998).

Similarly, the present invention demonstrates a combination of normalbases, unsubstituted pyrazolo[3,4-d]pyrimidine bases (e.g., PPG andPPA), 3-substituted pyrazolo[3,4-d]pyrimidines, modified purine,modified pyrimidine, 5-substituted pyrimidines, universal bases or aminor groove binder can be used to balance the T_(m) of anyoligonucleotide polymer or oligopolymer/DNA chimera.

For the uses described herein, the modified oligonucleotides willpreferably have from 4 to 70 bases, more preferably from 4 to 25 bases.In some embodiments, the modified oligonucleotides will have 15 orfewer, or more preferably 10 or fewer bases. Additionally, the modifiedoligonucleotides will, in some embodiments, have 3, 4, 5, 6, 7, 8, or 9or more modified bases (either unsubstituted or 3-substitutedpyrazolo[3,4-d]pyrimidines). For each of the embodiments whereinmultiple 3-substituted pyrazolo[3,4-d]pyrimidine bases are present, themodified bases can either be the same or different from each other.

In addition to the modified base components, the modifiedoligonucleotides of the present invention will in some embodimentscomprise additional pendant groups such as, for example, intercalators,lipophilic groups, minor groove binders, reporter groups, chelatingagents, quenchers and cross-linking agents attached to one or more ofthe internally located nucleotide bases, to the 3′, to the 5′ end, toboth ends, or can have such pendant groups attached both internally andat one or both ends. Methods suitable for attaching intercalator,lipophilic groups, minor grove binders, reporter groups, chelatingagents, quenchers and cross-linking agents to oligonucleotides have beendescribed in, for example, U.S. Pat. Nos. 5,512,667 and 5,419,966, PCTpublication WO 96/32496 and U.S. application Ser. No. 09/457,616. Theoligonucleotides of the invention can also have a relatively lowmolecular weight “tail moiety” attached either at the 3′ or 5′ end, orat both ends. By way of example a tail molecule can be a phosphate, aphosphate ester, an alkyl group, an aminoalkyl group, or a lipophilicgroup. The tail moiety can also link the intercalators, lipophilicgroups, minor groove binders, reporter groups, chelating agents andcross-linking functionalities to the oligonucleotides of the invention.The nature of tail moieties and methods for obtaining oligonucleotideswith various tail moieties are also described in the above-referencedU.S. Pat. Nos. 5,512,667 and 5,419,966.

Minor Groove Binders

In one group of embodiments, the modified oligonucleotide will also havea covalently attached minor groove binder (MGB). A variety of suitableminor groove binders have been described in the literature. See, forexample, Kutyavin, et al. U.S. Pat. No. 5,801,155; Wemmer, D. E., andDervan P. B., Current Opinon in Structural Biology, 7:355-361 (1997);Walker, W. L., Kopka, J. L. and Goodsell, D. S., Biopolymers, 44:323-334(1997); Zimmer, C & Wahnert, U. Prog. Biophys. Molec. Bio. 47:31-112(1986) and Reddy, B. S. P., Dondhi, S. M., and Lown, J. W., Pharmacol.Therap., 84:1-111 (1999).

Suitable methods for attaching MGBs (as well as reporter groups such asfluorophores and quenchers described below) through linkers tooligonucleotides are described in, for example, U.S. Pat. Nos.5,512,677; 5,419,966; 5,696,251; 5,585,481; 5,942,610 and 5,736,626.

The MGB can be attached at either or both ends of the oligonucleotide.In addition or alternatively, one or more MGBs can be attached in theinterior of the oligonucleotide, depending on the length of theoligonucleotide. In general, conjugation of a MGB to either end of anoligonucleotide would provide the greatest degree of hybrid stability,since melting of an oligonucleotide duplex begins at the termini.Nonetheless, if both ends of a duplex formed by an oligonucleotide arerelatively stable, for example, due to a high G+C content, attachment ofa MGB in the interior of an oligonucleotide (for instance, near anA+T-rich sequence) could also enhance stability. The intended use of theMGB-oligonucleotide conjugate may also place limitations on the locationof the conjugated MGB. For example, if an oligonucleotide is designed tobe used as a primer, the 3′-hydroxy group must be free and capable ofbeing elongated by a polymerizing enzyme. Alternatively, an assay thatrequires an oligonucleotide possessing a labeled 5′-end would requireinternal or 3′-end attachment of a MGB.

The location of a MGB within a MGB-modified oligonucleotide conjugatecan also affect the discriminatory properties of such a conjugate. Anunpaired region within a duplex will result in changes in the shape ofthe minor groove in the vicinity of the mispaired base(s). Since MGBsfit best within the minor groove of a perfectly-matched DNA duplex,mismatches resulting in shape changes in the minor groove would reducebinding strength of a MGB to a region containing a mismatch. Hence, theability of a MGB to stabilize such a hybrid would be decreased, therebyincreasing the ability of a MGB-oligonucleotide conjugate todiscriminate a mismatch from a perfectly-matched duplex. On the otherhand, if a mismatch lies outside of the region complementary to aMGB-oligonucleotide conjugate, discriminatory ability for unconjugatedand MGB-conjugated oligonucleotides of equal length is expected to beapproximately the same. Since the ability of an oligonucleotide probe todiscriminate single base pair mismatches depends on its length, shorteroligonucleotides are more effective in discriminating mismatches. Theprimary advantage of the use of MGB-oligonucleotides conjugates in thiscontext lies in the fact that much shorter oligonucleotides compared tothose used in the prior art (i.e., 20-mers or shorter), having greaterdiscriminatory powers, can be used, due to the pronounced stabilizingeffect of MGB conjugation.

Preferred minor groove binders are those selected from the formulae:

the subscript m is an integer of from 2 to 5; the subscript r is aninteger of from 2 to 10; and each R^(a) and R^(b) is independently alinking group to the modified oligonucleotide, H, —OR^(c), —NR^(c)R^(d),—COOR^(c) or —CONR^(c)R^(d), wherein each R^(c) and R^(d) is selectedfrom H, (C₁-C₁₂)heteroalkyl, (C₂-C₁₂)heteroalkenyl,(C₂-C₁₂)heteroalkynyl, (C₁-C₁₂)alkyl, (C₂-C₁₂)alkenyl, (C₂-C₁₂)alkynyl,aryl(C₁-C₁₂)alkyl and aryl.

Particularly preferred minor groove binders include the trimer of3-carbamoyl-1,2-dihydro-(3H)-pyrrolo[3,2-e]indole-7-carboxylate (CDPI₃),the pentamer of N-methylpyrrole-4-carbox-2-amide (MPC₅) and other minorgroove binders that exhibit increased mismatch discrimination.Additional MGB moieties that will find use in the practice of thepresent invention are disclosed in co-owned U.S. Pat. No. 5,801,155. Incertain embodiments, the MGBs can have attached watersolubility-enhancing groups (e.g., sugars or amino acids).

Reporter Groups

In another group of embodiments, the modified oligonucleotide willfurther comprise at least one covalently attached reporter group. Thereporter groups can be attached using methods and linking groupsdescribed above for the MGBs. Suitable reporter groups for the presentmodified oligonucleotides include beads, nanoparticles (Taton, T. A. etal, Science 289:1757-1760 (2000)), chemiluminescers, isotopes, enzymesand fluorophores. Preferably, the reporter group is a fluorophore (see,Haugland, R. P., HANDBOOK OF FLUORESCENT PROBES AND RESEARCH CHEMICALS,Sixth Edition, Molecular Probes, Eugene, Oreg., 1996). Suitablefluorophores include the resorufin dyes, coumarin dyes, rhodamine dyes,cyanine dyes, BODIPY dyes and pyrenes.

Quenchers

Recently developed detection methods employ the process of fluorescenceresonance energy transfer (FRET) for the detection of probehybridization rather than direct detection of fluorescence intensity. Inthis type of assay, FRET occurs between a donor fluorophore (reporter)and an acceptor molecule (quencher) when the absorption spectrum of thequencher molecule overlaps with the emission spectrum of the donorfluorophore and the two molecules are in close proximity. Theexcited-state energy of the donor fluorophore is transferred to theneighboring acceptor by a resonance dipole-induced dipole interaction,which results in quenching of the donor fluorescence. If the acceptormolecule is a fluorophore, its fluorescence may sometimes be increased.The efficiency of the energy transfer between the donor and acceptormolecules is highly dependent on distance between the molecules.Equations describing this relationship are known. The Forster distance(R_(o)) is described as the distance between the donor and acceptormolecules where the energy transfer is 50% efficient. Other mechanismsof fluorescence quenching are also known, such as, collisional andcharge transfer quenching. There is extensive guidance in the art forselecting quencher and fluor pairs and their attachment tooligonucleotides (Haugland, R. P., HANDBOOK OF FLUORESCENT PROBES ANDRESEARCH CHEMICALS, Sixth Edition, Molecular Probes, Eugene, Oreg.,1996; U.S. Pat. Nos. 3,996,345 and 4,351,760 and the like).

Preferred quenchers are described in co-owned U.S. Ser. No. 09/457,616(filed Dec. 8, 1999).

Fluorophores and Quenchers

In certain embodiments of the present invention, oligonucleotidescomprising fluorescent labels (fluorophores) and/or fluorescencequenching agents are used. In a preferred embodiment, an oligonucleotidecontains both a fluorophore and a quenching agent. Fluorescent labelsinclude, but are not limited to, fluoresceins, rhodamines, cyanines,phycoerythrins, and other fluorophores as described herein. Still othersuitable fluorophores are known to those of skill in the art. As notedabove, quenching agents or quenchers can absorb energy emitted by afluorophore so as to reduce the amount of fluorescence emitted (i.e.,quench the emission of the fluorescent label). Different fluorophoresare quenched by different quenching agents. In general, the spectralproperties of a particular fluorophore/quenching agent pair are suchthat one or more absorption wavelengths of the quencher overlaps one ormore of the emission wavelengths of the fluorophore. A preferredfluorophore/quencher pair can be selected by one of skill in the art bycomparison of emission and excitation wavelengths according to theproperties set forth above.

For use in amplification assays conducted at elevated temperatures, suchas a polymerase chain reaction, or other procedures utilizingthermostable enzymes, the label is preferably one that is stable atelevated temperatures. For assays involving polymerization, the label isone that does not interfere with the activity of the polymerizingenzyme. Additionally, the label will be present at the 5′ and/or 3′ endof the oligonucleotide, and/or can also be present internally in anon-interfering position. Accordingly, the label can be attached to anyof the bases, sugars or phosphate moieties of the oligonucleotide, or toany linking group that is itself attached to one of these moieties.

While the invention has been described in terms of the various bases andother optional components, the overall structure of the modifiedoligonucleotides can also be expressed in a formula to indicate adesired construction.

Thus, in one group of embodiments, the modified oligonucleotides havethe formula:

wherein R² and R³ represent the termini of the modified oligonucleotide;the subscript n is an integer of from 4 to 70, more preferably 4 to 25and still more preferably 4 to 10; each B is a member independentlyselected from adenine, thymine, cytosine, guanine, uracil, anunsubstituted pyrazolo[3,4-d]pyrimidine and a 3-substitutedpyrazolo[3,4-d]pyrimidine; and each M is selected from anoligomer-forming sugar and a peptide-nucleic acid-forming amino acid,with the proviso that at least two of the Bs are selected fromunsubstituted pyrazolo[3,4-d]pyrimidines and a 3-substitutedpyrazolo[3,4-d]pyrimidines. In certain specific embodiments, R² and R³represent the 5′- and 3′-ends of a modified oligonucleotides wherein Mis an oligomer-forming sugar (e.g., 2-deoxy-β-D-ribofuranose,β-D-ribofuranose, α-D-arabinofuranosides, α-2′-deoxyribofuranosides,2′,3′-dideoxy-3′-aminoribofuranosides, and locked sugars). For thoseembodiments in which the modified oligonucleotides have attached minorgroove binders, reporter groups, etc., each of the R² and R³ groups aremeant to include functional groups suitable for attachment of linkinggroups and the additional functional component (MGB, fluorophore,quencher, and the like). Such functional groups include, for example,hydroxy groups, amino groups, carboxylic acid or ester groups,phosphoric, phosphonic, or phosphinic acid or ester groups, sulfonicacid and ester groups, and the like. In other embodiments, MGBs,reporter groups and the like are attached to any of the interiorbase/backbone groups using conventional methodology.

In a related aspect, the present invention provides modifiedoligonucleotides comprising at least one 5-substituted pyrimidine baseand at least one unsubstituted or 3-substitutedpyrazolo[3,4-d]pyrimidine base. The unsubstituted or 3-substitutedpyrazolo[3,4-d]pyrimidine bases useful in this aspect of the inventionare essentially those that have been described above (see formulae Iaand Ib). A variety of 5-substituted pyrimidine bases are usefulincluding those described in U.S. Pat. Nos. 5,645,985 and 5,484,908.

In preferred embodiments, the 5-substituted pyrimidine base has theformula:

and the unsubstituted or 3-substituted pyrazolo[3,4-d]pyrimidine basehas the formula:

wherein each of the X¹, X² and X³ groups is independently selected fromH, OH, NH₂ and a protected amino group; and each of the R¹ and R⁴ groupsis independently selected from (C₁-C₁₂)heteroalkyl,(C₂-C₁₂)heteroalkenyl, (C₂-C₁₂)heteroalkynyl, —O—(C₁-C₁₂)alkyl,—O—(C₂-C₁₂)alkenyl, —O—(C₂-C₁₂)alkynyl, —S—(C₁-C₁₋₂)alkyl,—S—(C₂-C₁₂)alkenyl, —S—(C₂-C₁₂) heterocyclyl(C₁-C₁₂)alkyl,heterocyclyl(C₂-C₁₂)alkenyl, heterocyclyl(C₂-C₁₂)alkynyl,aryl(C₁-C₁₂)alkyl, aryl(C₂-C₁₂)alkenyl, aryl(C₂-C₁₂)alkynyl, aryl,heterocyclyl, halogen, —CN, —CONH₂ and protected forms thereof, with theadditional feature that R¹ can also be H.

In particularly preferred embodiments, the 5-substituted pyrimidine baseis selected from:

wherein R⁴ is preferably selected from propynyl, hydroxypropynyl,aminopropynyl, hydroxybutynyl or a substituted or unsubstituted phenyl,thienyl, thiazolyl, imidazolyl, furanyl, oxazolyl, pyridinyl, pyrrolyl,indolyl, benzimidazolyl, benzthiazolyl or benzoxazolyl group attacheddirectly to the pyrimidine ring or attached to the ring via a one tofour carbon linking group which can be saturated (e.g., ethylene,propylene, butylene) or unsaturated (e.g., acetylenyl, propynylene,butynylene, propenylene, butenylene).

In other preferred embodiments, the pyrazolo[3,4-d]pyrimidine base isselected from the preferred bases provided above (Ic, Id and Ie).Additionally, suitable bases are also depicted in FIG. 1.

As with the earlier aspect of the invention wherein the modifiedoligonucleotides comprise at least two unsubstituted or 3-substitutedpyrazolo[3,4-d]pyrimidines, this aspect of the invention can similarlycomprise additional groups such as MGBs and reporter groups (e.g.,fluorophores, quenchers and the like) as well as linking groups suitablefor the attachment of these additional components.

Also preferred are those embodiments in which the modifiedoligonucleotide is represented by the formula:

wherein R² represents a first end of the modified oligonucleotide; R³represents a second end of the modified oligonucleotide; the subscript nis an integer of from 4 to 70; each B is independently selected fromadenine, thymine, cytosine, guanine, uracil, a 5-substituted pyrimidine,an unsubstituted pyrazolo[3,4-d]pyrimidine and a 3-substitutedpyrazolo[3,4-d]pyrimidine (with the proviso that at least one base is a5-substituted pyrimidine and at least one base is apyrazolo[3,4-d]pyrimidine); and each M is an oligomer-forming sugar or apeptide-nucleic acid-forming amino acid.

In yet another aspect of the invention, modified oligonucleotides areprovided which comprise an attached minor groove binder and in which asfew as one of the bases is replaced with a modified base. Surprisingly,the combination of MGBs and a single modified base (or optionallymultiple modified bases) leads to modified oligonucleotides havingparticularly useful properties for mismatch discrimination as well asprimer extesions and other utilities described below. This group ofmodified oligonucleotides preferably comprise from 4 to 70 bases, and anattached minor groove binder, wherein at least one of the bases isreplaced by a modified base selected from the group consisting of5-substituted pyrimidines and unsubstituted or 3-substitutedpyrazolo[3,4-d]pyrimidines.

In this aspect of the invention, the minor groove binders, 5-substitutedpyrimidines and unsubstituted or 3-substitutedpyrazolo[3,4-d]pyrimidines can be essentially any of those componentsdescribed above.

In one group of embodiments, the modified oligonucleotide has at leastone 5-substituted pyrimidine, preferably having the formula:

wherein X³ is selected from H, NH₂, OH and SH; and R⁴ is selected from(C₁-C₁₂)heteroalkyl, (C₂-C₁₂)heteroalkenyl, (C₂-C₁₂)heteroalkynyl,—O—(C₁-C₁₂)alkyl, —O—(C₂-C₂)alkenyl, —O—(C₂-C₁₂)alkynyl,—S—(C₁-C₁₂)alkyl, —S—(C₂-C₁₂)alkenyl, —S—(C₂-C₁₂) alkynyl,heterocyclyl(C₁-C₁₂)alkyl, heterocyclyl(C₂-C₁₂)alkenyl,heterocyclyl(C₂-C₁₂)alkynyl, aryl(C₁-C₁₂)alkyl, aryl(C₂-C₁₂)alkenyl,aryl(C₂-C₁₂)alkynyl, aryl, heterocyclyl, halogen, —CN, —CONH₂ andprotected forms thereof. In this group of embodiments, preferred aryland heterocyclyl group (including those components of other groups,e.g., arylalkyl) are selected from substituted and unsubstitutedversions of phenyl, tolyl, pyridyl, thiazolyl, imidazolyl, furanyl,oxazolyl, thienyl, pyrrolyl, benzimidazolyl, benzoxazolyl,benzthiazolyl, indolyl, triazinyl, pyrimidinyl and naphthyl. Suitablesubstituents for these aryl and heterocyclyl groups are those providedin the general definitions above.

More preferably, the modified oligonucleotides comprise at least one5-substituted pyrimidine based group of Formula IId and IIe, where theR⁴ substituent group is selected from a substituted or unsubstitutedalkyl group or alkynyl group. Preferably, R⁴ is a hydroxypropynyl,hydroxybutynyl, aminopropynyl, aminobutynyl or propynyl group, as wellas the higher homologs (e.g., C₅-C₈) of these alkynyl groups.Alternatively, the R⁴ substituent can be a3-(hydroxymethyl)-4-hydroxy-1-butynyl group (described in more detailbelow).

In another group of preferred embodiments, the modified oligonucleotidehas at least one modified base having the formula:

wherein each of the X¹ and X² groups is independently selected from H,OH, NH₂ and a protected amino group; and R¹ is selected from H,(C₁-C₁₂)heteroalkyl, (C₂-C₁₂)heteroalkenyl, (C₂-C₁₂)heteroalkynyl,—O—(C₁-C₁₂)alkyl, —O—(C₂-C₁₂)alkenyl, —O—(C₂-C₁₂)alkynyl,—S—(C₁-C₁₂)alkyl, —S—(C₂-C₁₂)alkenyl, —S—(C₂-C₁₂)alkynyl, heterocyclylC₁-C₁₂)alkyl, heterocyclyl(C₂-C₁₂)alkenyl, heterocyclyl(C₂-C₁₂)alkynyl,aryl(C₁-C₁₂)alkyl, aryl(C₂-C₁₂)alkenyl, aryl(C₂-C₁₂)alkynyl, aryl,heterocyclyl, halogen, —CN, —CONH₂ and protected forms thereof. In thisgroup of embodiments, preferred aryl and heterocyclyl group (includingthose components of other groups, e.g., arylalkyl, heterocyclylalkyl)are selected from substituted and unsubstituted versions of phenyl,tolyl, pyridyl, thiazolyl, imidazolyl, furanyl, oxazolyl, thienyl,pyrrolyl, benzimidazolyl, benzoxazolyl, benzthiazolyl, indolyl,triazinyl, pyrimidinyl and naphthyl. Suitable substituents for thesearyl and heterocyclyl groups are those provided in the generaldefinitions above.

In particularly preferred embodiments, the modified oligonucleotidescomprise at least one monomer of formula If,

wherein X¹ and X² are independently H, OH or NH₂; and R¹ is mostpreferably 3-hydroxypropyn-1-yl, propynyl, 3-aminopropyn-1-yl,4-hydroxy-1-butynyl, 3-(hydroxymethyl)-4-hydroxy-1-butynyl, halogen or3,3,3-trifluoropropyn-1-yl. Syntheses of some of these monomers havebeen reported (Balow et al., Nuc. Acid Res., 26:3350-3357 (1998); Seelaet al., J. Chem. Soc. Perkin Trans., I, 479-488 (1999); Ramzaeva et al.,Helv. Chim. Acta, 80:1809-1822 (1997)).Preparation of Modified Bases and Oligonucleotides

Reaction Schemes 1-10 provide illustrative methods for preparing anumber of modified bases (unsubstituted and 3-substitutedpyrazolo[3,4-d]pyrimidines and 5-substituted pyrimidines) that areuseful in the present invention. The schemes illustrate the preparationof phosphoramidite derivatives of the modified bases which can be usedin, for example, automatic synthesizers for preparing the modifiedoligonucleotides of the invention.

Reaction Scheme I illustrates the preparation of5-(prop-2-ynyl-4-methylbenzoate)-5′-O-(4,4′-dimethoxytriphenylmethyl)-2′-deoxyuridine3′-[(2-cyanoethyl) N,N-diisopropylphosphoramidite] (3) starting from5-iodo-2′-deoxyuridine. The starting materials was treated withprop-2-ynyl 4-methylbenzoate in the presence of Pd(PPh₃)₄—CuI to yieldthe methylbenzoate derivative (1) which was then converted to the5′-blocked DMTr derivative (2) and then to the phosphoramidite (3).

Reaction Schemes 2 and 3 provide one method for the preparation ofpyrazolo[3,4-d]pyrimidine phosphoramidites. More particularly, theseschemes illustrate the preparation of3-[-4((1E)-1-aza-2-methylprop-1-enyl)-1-((2R,5R)-4-{[bis(methylethyl)amino](2-cyanoethoxy)phosphinooxy}-5-{[bis(4-methoxyphenyl)phenylmethoxy]methyl}oxolan-2-yl)pyrazolo[3,4-d]pyrimidin-3-yl]prop-2-ylnyl4-methylbenzoate (13; R₁=—OCOPhCH₃) is synthesized in two portions.

In the first portion (Reaction Scheme 2),(2R,5R)-5-(4-amino-3-iodopyrazolo[3,4-d]pyrimidinyl)-2-(hydroxymethyl)oxolan-3-ol(9) was synthesized starting from1,5-hydropyrazolo[3,4-d]pyrimidin-4-one. The starting material wastreated with iodine monochloride and P₂S₅ successively to yield the iodo(4) and thione (5) derivatives respectively. The thione (5) wasconverted to the ethylthio-derivative (6), which was combined with a1-chloro-1,2-dideoxy-3,5-di-O-toluoylribofuranose derivative to yieldthe blocked nucleoside (7). Reaction of compound (7) with sodiummethoxide followed by ammonium hydroxide gave hydroxymethyl derivative(8) and compound (9) respectively.

In the second portion (Reaction Scheme 3),2,3-[-4((1E)-1-aza-2-methylprop-1-enyl)-1-((2R,5R)-4-{[bis(methylethyl)amino](2-cyanoethoxy)phosphinooxy}-5-{[bis(4-methoxyphenyl)phenylmethoxymethyl}oxolan-2-yl)pyrazolo[3,4-d]pyrimidin-3-yl]prop-2-ylnyl4-methylbenzoate (13 R₁═—OCOPhCH₃) was prepared starting from compound(9). Compound (9) was reacted with prop-2-ynyl 4-methylbenzoate in thepresence of Pd(PPh₃)₄—CuI to yield the prop-2-ynyl derivative (10;R₁═—OCOPhCH₃). The amino group in this compound was protected byreaction with N,N dimethylacetamide dimethyl acetal to give(11;R₁,═—OCOPhCH₃). Compound (11; R₁=—OCOPhCH₃) was converted to theDMTr derivative (12; R₁═—OCOPhCH₃) and then to the phosphoramidite (13;R₁═—OCOPhCH₃).

Reaction Scheme 4 illustrates the preparation ofN-{3-[1-((2R,5R)-5-{bis(4-methoxyphenyl)phenylmethoxymethyl}-4-{[bis(methylethyl)amino](2-cyanoethoxy)phosphinooxy}oxolan-2-yl)-6-amino-4-oxo(5-hydropyrazolo[3,4-d]pyrimidin-3-yl)]propyl}-2,2,2-trifluoroacetamide(22).

In Reaction Scheme 4,6-amino-4-methoxypyrazolo[3,4-d]pyrimidine wasconverted to the iodo derivative (14) which was treated with1-chloro-1,2-dideoxy-3,5-di-O-toluoylribofuranose to yield thenucleoside (15). Compound (15) was treated with NaOMe/MeOH to hydrolyzethe toluoyl groups and yield the unblocked nucleoside (16). Treatment of(16) with aqueous sodium hydroxide gave (17) which could be converted tothe trifluoro-N-prop-2-ynyl acetamide derivative (18). Compound (18) wasreduced with hydrogen and a Pd catalyst to yield thetrifluoro-N-propylacetamide derivative (19). The 4-amino group ofcompound (19) was protected by treatment with N,N-dimethylformamidedimethylacetal to give compound (20) which was converted to DMTrderivative (21) and then to the phosphoramidite derivative (22).

Compounds of Formula 4(3-[((2R,5R)-5-(6-amino-4-oxo-3-prop-1-ynyl(5-hydropyrazolo3,4-d]pyrimidinyl))-2-{[bis(4-methoxyphenyl)phenylmethoxy]-methyl}oxolan-3-yloxy)[bis(methylethyl)amino]phosphinooxy]propanenitrile)(PPPG phosphoramidite) can be synthesized using some of the reactions inReaction Scheme 4.

In the conversion of (17) to (18), prop-1-yne is used in place of2,2,2-trifluoro-N-prop-2-ynylacetamide. The 6-amino group can beprotected as described for compound (20) and the 5′-hydroxyl can beprotected with a DMTr group as described for compound (21). Finally thephosphoramidite can be prepared as described for compound (22) to yieldthe compound of Formula 4. In a similar way compounds of Formula 5 whereR⁶ is —OCOPhCH₃ or —NHCOCF₃. can be prepared using related reactionsknown in the art.

Reaction Scheme 5 illustrates the preparation of3-{[5-(4,6-bis{(1E)-1-aza-2-[bis(2-methylpropyl)amino]vinyl}-3-prop-1-ynylpyrazolo[3,4-d]pyrimidinyl)-2-{[bis(4-methoxyphenyl)phenylmethoxy]-methyl}oxolan-3-yloxy][ethyl(methylethyl)amino}-phosphino)propanenitrile(26).

Compound (26) can be synthesized starting from (NH₂)₂PPPA (23) (see,Seela & Driller, Helv. Chim. Acta 71:757-761(1988)). Compound (23) canbe converted to the bis(methylethyl)amino derivative (24) (Vincent etal, J. Org. Chem., 64:991-997 (1999)), followed by reaction first withDMTrCl to yield (25) that can be converted to the phosphoramidite (26).

Reaction Scheme 6 provides the synthesis of protected 3-substitutedpyrazolo[3,4-d]pyrimidines in which the substituent is a heteroalkylgroup.

Reaction Scheme 7 provides the synthesis of protected 3-substitutedpyrazolo[3,4-d]pyrimidine in which the substituent is a methoxypropynylgroup. The 3-iodo diamino derivative (23) was reacted withPd(PPh₃)₄—CuI, triethylamine in anhydrous DMF followed by methylpropargyl ether to yield the3-methoxypropynyl-2,4-diaminopyrazolo[3,4-d]pyrimidine derivative (27).The amino groups in this compound were blocked by reaction withN,N-dimethylformamide dimethylacetal to yield (28). The blockednucleoside was first reacted with dimethoxytrityl chloride and then with2-cyanoethyl diisopropylchlorophosphoramidite to yield the desiredblocked phosphoramidite (29).

The following reaction schemes provide methods for the preparation of3-heterocycle substituted pyrazolo[3,4-d]pyrimidines. The generalmethods provided herein can be adapted for the preparation of otherheterocyclic substituents.

Reaction Scheme 8 provides the synthesis of protected 3-substitutedpyrazolo[3,4-d]pyrimidine in which the substituent is a furanyl group.Malonitrile was reacted with 2-furfuryl chloride in the presence of abase, followed by treatment with dimethylsulfide to give the methoxydinitrile derivative (30). Reaction of (30) with hydrazine yielded thesubstituted pyrazole (31) which was reacted with formamide to give3-(2-furyl)pyrazolo[3,4-d]pyrimidine-4-ylamine (32). Base (32) wastreated with 1-chloro-1,2-dideoxy-3,5-di-O-toluoylribofuranose to yieldthe blocked nucleoside (33). Compound (33) was first treated withNaOMe/MeOH to hydrolyze the toluoyl groups to yield the unblockednucleoside which was reacted with N,N-dimethylformamide dimethylacetalto yield the protected nucleoside derivative (34). This derivative wasfirst reacted with dimethoxytrityl chloride and then with 2-cyanoethyldiisopropylchlorophosphoramidite to yield the desired blockedphosphoramidite (35).

Reaction Scheme 9 provides the synthesis of protected 3-substituted2,4-diamino pyrazolo[3,4-d]pyrimidine in which the substituent is afuranyl group. The carbonitrile (31) was reacted with guanidiniumcarbonate to yield 3-(2-furyl)pyrazolo[3,4-d]pyrimidine-4,6-diamine(36). This base was treated with1-chloro-1,2-dideoxy-3,5-di-O-toluoylribofuranose to yield the blockednucleoside which was treated with NaOMe/MeOH to hydrolyze the toluoylgroups and yield the unblocked nucleoside derivative (37). The lattercompound was reacted with N,N-dimethylformamide dimethylacetal to yieldthe protected nucleoside derivative (38). This derivative was firstreacted with dimethoxytrityl chloride and then with 2-cyanoethyldiisopropylchlorophosphoramidite to yield the desired blockedphosphoramidite (39).

Reaction Scheme 10 provides one synthesis route to a hydroxy-protectedHOBU-phosphoramidite. In this scheme, 3-butyn-1-ol is converted to itsp-toluoyl ester (40) with p-toluoyl chloride in the presence ofpyridine. The protected butynol is combined with 5-iodo-2′-deoxyuridinein the presence of tetrakis(triphenylphosphine)palladium(0) and copperiodide, then protected (as a DMT ether) to form 41, which can then beconverted to its corresponding phosphoramidite derivative 42. Reagent 42can be used directly in the preparation of modified oligonucleotides.Removal of the p-toluoyl protected group can be accomplished accordingto standard methods.

In each of the above schemes, one of skill in the art will understandthat other protecting groups and/or activating groups can be used.Additionally, different non-natural base-containing monomers, withdifferent functional groups, can require different blocking groups forsuccessful synthesis of the modified oligonucleotides. A variety ofuseful protection groups, their synthesis and de-protection methods aredescribed in, for example, Beaucage & Iyer, Tetrahedron 48:2223-2311(1992).

The synthesis of oligonucleotides, and modified oligonucleotides can beinitiated from a solid support containing a cleavable linker to which isattached the first base. The oligonucleotides of the invention can besynthesized containing a substituted pyrazolo[3,4-d]pyrimidine as thefirst nucleotide at the 3′-end, using an appropriate 3-substitutedpyrazolo[3,4-d]pyrimidine. Alternatively, a 5-substituted pyrimidine canbe attached initially to a solid support. Reaction Scheme 11 illustratesa general approach to the synthesis of a protected 3-substitutedpyrazolo[3,4-d]pyrimidine dA CPG derivative (C). Intermediate (A) can beprepared using procedures described in Reaction Scheme 3, while (B) and(C) can be synthesized as described in co-pending U.S. application Ser.No. 09/457,616.

In this aspect of the invention, a variety of solid supports are useful,provided the support is compatible with automated oligonucleotidetechniques and include, glass, polystyrene, nylon, plastic and the like.Additionally, the present invention provides in a related aspect, asolid support (e.g., controlled pore glass (CPG)) having an attachedmodified base, preferably those of formulae Ic, Id, Ie, If, IIb, IIc,IId, IIe. More preferably, the attached modified base is a 3-substitutedpyrazolo[3,4-d]pyrimidine or a 5-substituted pyrimidine moiety whereinthe substituents are selected from the preferred groups described above,and further including the novel bases described in more detail below.

The present invention further includes those compositions and methodswherein any of the unsubstituted and/or 3-substitutedpyrazolo[3,4-d]pyrimidines and/or 5-substituted pyrimidines are combinedor used in combination with other modified bases known in the art. Othermodified modified monomeric units have been disclosed Scheit, NUCLEOTIDEANALOGS, John Wiley, New York, 1980; Uhlman and Meyman, ChemicalReviews, 90:543-584 (1990), Seela and Debelak, Nucl. Acids Res.,28:3224-3232 (2000); Balow et al, Nucl. Acids Res., 26:3350-3357 (1998);Bolli et al Nucl. Acids Res., 24:4660-4667 (1996).

Modified Oligonucleotide Arrays

In another embodiment of the present invention, modifiedoligonucleotides are used in procedures which utilize arrays ofoligonucleotides, such as sequencing by hybridization and array-basedanalysis of gene expression. A variety of arrays are contemplated by thepresent invention including, for example, chip or platform arrays, beadarrays, liquid phase arrays, ‘zip-code’ arrays and the like. Insequencing by hybridization, an ordered array of oligonucleotides ofdifferent known sequences is used as a platform for hybridization to oneor more test polynucleotides, nucleic acids or nucleic acid populations.Determination of the oligonucleotides which are hybridized and alignmentof their known sequences allows reconstruction of the sequence of thetest polynucleotide. Alternatively, oligonucleotides comprising thewild-type sequence and all possible mutant sequences for a given regionof a gene of interest can be placed on an array. Exposure of the arrayto DNA or RNA from a subject or biological specimen, under hybridizationconditions, allows determination of wild-type or mutant status for thegene of interest. See, for example, U.S. Pat. Nos. 5,492,806; 5,525,464;5,556,752; and PCT Publications WO 92/10588 and WO 96/17957. Both ofthese techniques require discrimination between related sequences,especially at the single-nucleotide level; hence, the enhanceddiscriminatory properties of the modified oligonucleotides of theinvention will provide improvements in these techniques. Materials forconstruction of arrays include, but are not limited to, nitrocellulose,glass, silicon wafers, optical fibers and other materials suitable forconstruction of arrays such as are known to those of skill in the art.The synthesis of oligonucleotides arrays has been described inco-pending U.S. application Ser. No. 09/364,320, and suitablemodifications can be made to the methods therein for preparing thearrays of the present invention.

An additional application of the present invention to array technologyis in the examination of patterns of gene expression in a particularcell or tissue. In this case, oligonucleotides or polynucleotidescorresponding to different genes are arrayed on a surface, and a nucleicacid sample from a particular cell or tissue type, for example, isincubated with the array under hybridization conditions. Detection ofthe sites on the array at which hybridization occurs allows one todetermine which oligonucleotides have hybridized, and hence which genesare active in the particular cell or tissue from which the sample wasderived.

Array methods can also be used for identification of mutations orpolymorphisms, where wild-type and mutant sequences are placed in anordered array on a surface. Hybridization of a polynucleotide sample tothe array under stringent conditions, and determination of whicholigonucleotides in the array hybridize to the polynucleotide, allowsdetermination of whether the polynucleotide possesses the wild-type orthe mutant sequence. Since many mutant sequences of clinically-relevantgenes differ from their wild-type counterpart at only one or a fewnucleotide positions, the enhanced discriminatory powers of the modifiedoligonucleotides of the invention will provide improvements in mutationdetection.

In all of the above-mentioned applications of array technology, theincreased discriminatory abilities of modified oligonucleotide providesignificant improvements in sensitivity and resolving power.

Efficient hybridization, for example in arrays, requires that thecapture probes contain T_(m)'s in a narrow temperature range. In oneembodiment of the invention the T_(m) of capture oligonucleotides foruse in arrays is balanced, eliminating the problem associated with GCand AT-rich sequences, by using a combination of 3′-MGBs and modifiedbases (e.g., PPPA and PPPU). Table 1 and FIG. 2 illustrate the balancingof the T_(m) of pyrimidine rich probes with different G/C and A/T basepairs. To balance the T_(m) of the different probes, PPPA, PU and MGBwere used in combination. The purine and pyrimidine-rich probes andcomplementary targets are shown in Table 1 and the T_(m)s these probesare shown in FIG. 2. As shown in FIG. 2 the T_(m) difference between aGC-rich and an AT-rich probe can be more than 50° C.

TABLE 1 Sequences of Oligonucleotide Probes and Complementary TargetsComplementa- SEQ ID base ry Targets NO: Py/Pu-rich probes pairs 1*TCGGCGGCGT 8 1*.MGB-Q-CGCCGCCG 8 G/C 2* ACAGCGGCGT 9 2* MGB-Q-CGCCGCTG 7G/C, 1 A/T 3* ACAGCGACGT 10 3*.MGB-Q-CGTCGCTG 6 G/C, 2 A/T 4* TCAGTGACGA11 4*.MGB-Q-CGTCACTG 5 G/C, 3 A/T 5* TCAGTGACAA 12 5*.MGB-Q-TGTCACTG 4G/C, 4 A/T 6* TCAATGACAG 13 6*.MGB-Q-TGTCATTG 3 G/C, 5 A/T 7* ACAATGATAA14 7*.MGB-Q-TATCATTG 2 G/C, 6 A/T 8* CCAATAATAA 15 8*.MGB-Q-TATTATTG 1G/C, 7 A/T 9* GTAATAATAA 16 9*.MGB-Q-TATTATTA 8 A/T

As can be seen in FIG. 2, modification with PPPA, PU and a MGB providesa probe set having balanced T_(m)s.

Efficient hybridization for example in arrays, requires that the probescontain T_(m)'s in a narrow temperature range. Thus, in relatedembodiments, the modified oligonucleotides described herein can compriseany combination of normal bases, unsubstituted pyrazolo[3,4-d]pyrimidinebases (e.g., PPG and PPA), 3-substituted pyrazolo[3,4-d]pyrimidines,modified purine, modified pyrimidine, 5-substituted pyrimidines,universal bases and a minor groove binder to balance the T_(m) of theoligonucleotide.

The ability to predict and “level” the T_(m)s of multiple modifiedoligonucleotides is particularly useful for the development ofoligonucleotide arrays or for compositions having a plurality ofoligonucleotides. Still further, the ability to predict T_(m)s formodified oligonucleotides is useful for establishing appropriateconditions for hybridization, renaturation, mapping variations of basecompositions of sequences, determination of sequence complexity anddivergence. A T_(m) prediction algorithm can be developed using modelsthat assign thermodynamic contributions to duplex formation for allpossible individual base pair nearest neighbors. Thermodynamicparameters for 10 independent nearest-neighbors of base pairs areavailable from published sources for DNA:RNA hybrids (see Sugimoto etal., Biochem. 34:11211-11216 (1995)) and dsDNA (SantaLucia et al,Biochem. 36:10581-10595 (1997)). The use of the nearest neighborparameters to develop programs to calculate oligonucleotide duplexstability in terms of T_(m) have been described (see, Schutz & vonAhsen, Biotechniques, 27:1218-22 (1999); Owczarzy et al, Biopolymers,44:217-239 (1997); for PNA/DNA, see Geisen et al, Nucl. Acids Res.,26:5004-5006 (1998); Blake et al, Bioinformatics, 15:370-5 (1999) andU.S. Pat. No. 5,556,749.

The basic principles of thermodynamic and kinetic description ofmismatch discrimination are well known and are summarized below.

A probe-target interaction is an equilibrium reaction that can bedescribed as

A+B

AB where A=probe, B=DNA target

At the temperature T equilibrium of forward (association) and reverse(dissociation) reactions can be described by equilibrium constant Kwhere:

${K = \frac{\lbrack{AB}\rbrack}{\lbrack A\rbrack\lbrack B\rbrack}};$in terms of equilibrium thermodynamicsK=exp(−ΔH^(o) _(AB) /RT+ΔS ^(o) _(AB) /R);ΔG ^(o) _(AB) =ΔH ^(o) _(AB) −TΔ _(AB);ΔG ^(o) _(AB) =−RTLn(K)where: ΔH^(o) _(AB), ΔS^(o) _(AB) and ΔG^(o) _(AB)—enthalpy, entropy andfree energy changes for duplex AB formation.

The duplex AB has N base pairs (N−1 nearest neighbors) and thenearest-neighbor approximation assumesΔH ^(o) _(AB)=ΔH^(o) ₁ +ΔH ^(o) ₂ + . . . ΔH ^(o) _(n-1) +ΔH ^(o)_(init)=Σ(ΔH ^(o) _(i) +ΔH ^(o) _(init))ΔS ^(o) _(AB) =ΔS ^(o) ₁ +ΔS ^(o) ₂ + . . . ΔS ^(o) _(n-1) +ΔS ^(o)_(init)=Σ(ΔS ^(o) _(i) +ΔS ^(o) _(init))ΔG ^(o) _(AB) =ΔG ^(o) ₁ +ΔG ^(o) ₂ + . . . ΔG ^(o) _(n-1) +ΔG ^(o)_(init)=Σ(ΔG ^(o) _(i) +ΔG ^(o) _(init))where: ΔH^(o) _(i), ΔG^(o) _(i) and ΔG^(o) _(i)—enthalpy, entropy andfree energy changes for each nearest-neighbor base pairs increment forduplex AB formation, ΔH^(o) _(init), ΔS^(o) _(init) and ΔG^(o)_(init)—thermodynamic parameters of initiation of duplex AB formation.

In the case of total concentration equality, C_(probe)═C_(target), anequation for Tm in terms of free energy, enthalpy and entropy can bearrived at as shown below:

${TM} = \frac{\Sigma\left( {{\Delta\; H_{i}^{0}} + {\Delta\; H_{init}^{0}}} \right)}{{\Sigma\left( {{\Delta\; S_{i}^{0}} + {\Delta\; S_{init}^{0}}} \right)} + {{RLn}\left\lbrack {\left( {C_{probe} + C_{target}} \right)/4} \right\rbrack}}$

Similarly as shown above relationships can be developed when the probehybridizes to a target that contains a mismatch, as shown below:

A+B*

AB* A=probe, B*=mismatched DNA target

Thermodynamic parameters for mismatched duplex AB* are: K*, ΔH^(o)_(AB*), ΔS^(o) _(AB*) and ΔG^(o) _(AB*). In terms of nearest-neighborparameters for a mismatched base pair at position “4”, for example,involving nearest-neighbor “3” and “4” the discrimination parametersΔΔH^(o), ΔΔS^(o), ΔΔG^(o) can be expressed as:ΔΔH ^(o) =ΔH ^(o) _(AB) −ΔH ^(o) _(AB*)=(ΔH ^(o) ₃ −ΔH ^(o)*₃)+(ΔH ^(o)₄ −ΔH ^(o)*₄)=ΔΔH ^(o) ₃ ΔΔH ^(o) ₄.ΔΔS ^(o) =ΔS ^(o) _(AB) −ΔS ^(o) _(AB*)=(ΔS ^(o) ₃ −ΔS ^(o)*₃)+(ΔS ^(o)₄ −ΔS ^(o)*₄)=ΔΔS ^(o) ₃ +ΔΔS ^(o) ₄.ΔΔG ^(o) =ΔG ^(o) _(AB) −ΔG ^(o) _(AB*)=(ΔG ^(o) ₃ −ΔG ^(o)*₃)+(ΔG ^(o)₄ −ΔG ^(o)*₄)=ΔΔG ^(o) ₃ +ΔΔG ^(o) ₄.

In one embodiment of the invention, probe sequences are designed todetermine the thermodynamic nearest-neighbor parameters foroligonucleotides containing normal purines, pyrimidines and a minorgroove binder CDPI₃ attached to the 3′-end of an oligonucleotide. Inanother embodiment thermodynamic nearest-neighbor parameters foroligonucleotide containing normal pyrimidines, purines, a 3′-endattached CDPI₃, but wherein the guanine is replaced with5-hydropyrazolo[3,4-d]pyrimin-4-one. These nearest-neighborthermodynamic parameters are used in these two embodiments to calculatethe T_(m)s of these types of oligonucleotides with and without CDPI₃. Inthe case where the CDPI₃ was attached at base I at the 3′-end the newT_(m) prediction algorithm and formula were used as derived below.

${TM} = \frac{\Sigma\left( {{\Delta\; H_{i}^{0}} + {\Delta\; H_{init}^{0}}} \right)}{{\Sigma\left( {{\Delta\; S_{i}^{0}} + {\Delta\; S_{init}^{0}}} \right)} + {{RLn}\left\lbrack {\left( {C_{probe} + C_{target}} \right)/4} \right\rbrack} + {{\Delta\Delta}\; S_{MGB}^{0}}}$

The model assumes that a MGB attached to an oligonucleotide has anadditional pure entropic factor ΔΔS^(o) _(MGB). This value can becalculated according to algorithm: 6 bases (5 nearest-neighbor) from3′-prime end are covered by the MGB from starting base “1” or “2”. Eachnearest-neighbors covered has unique value ΔΔS^(o) _(iMGB). Correctionfactor “A” are introduced in the case when adenosine can be found inbase positions 6, 7 or 8. Statistical factor “n” is introducedadditionally to factor “A” were n=3 for -AAA-; n=2 for -AA-, -ANA-; n=1for -A-; n=0 for -AN- and -NA- (N is any base other than A). A finalvalue ΔΔS^(o) _(MGB) can be determined by the equationΔΔS ^(o) _(MGB) =ΣΔΔS ^(o) _(iMGB) +A(optional)+R*Ln(N) (optional)

Tables 2a and 2b contain the nearest-neighbor thermodynamic parametersfor oligonucleotides containing PPG alone and the entropic contributionof the MGB, respectively. In the latter case the contribution offluorescein and a dark quencher is incorporated in the thermodynamictreatment and has generally been shown to be negligible. [The quencheris part of the linker between the MGB and the oligonulceotide]

TABLES 2a AND 2b a) Nearest-neighbor parameters for PPG containingoligonucleotides b) The entropic contribution of the CDPI₃. a) Number5′-3′ ΔH° ΔS° ΔG°(65) 1 AA −7850 −22.3 −324 2 AT −8180 −23.0 −411 3 AC−8450 −22.6 −795 4 AG −6560 −17.2 −730 5 TA −7230 −21.8 129 6 TT −7850−22.3 −324 7 TC −8720 −24.0 −614 8 TG −6900 −18.3 −715 9 CA 7530 −20.3−652 10 CT −6390 −17.3 −548 11 CC −7860 −20.1 −1071 12 CG −6030 −14.0−1288 13 GA −10070 −27.4 −795 14 GT −9110 −23.5 −1175 15 GC −13170 −34.0−1665 16 GG −8080 −20.2 −1258 17 GCinit −48440 −17.6 1116 18 ATinit−1060 −7.1 1341 b) Number 5′-3′ ΔΔS° 1 AA 3.408 2 AT 3.060 3 AC 1.442 4AG 0.750 5 TA 2.463 6 TT 3.313 7 TC 2.870 8 TG 0.893 9 CA 0.607 10 CT2.253 11 CC 0.905 12 CG −0.721 13 GA 1.282 14 GT 2.397 15 GC 2.172 16 GG1.298

In one preferred embodiment T_(m)s of multiple modified oligonucleotidescontaining the same number of bases are leveled using an algorithm toselect nearest neighbor parameters from any combination of normal bases,universal bases, PPA, PPG, PPPA, PPPG, PU, PC, HOPU, HOBuU, HOBuC,(NH₂)₂PPPA, (NH₂)₂PPPAOH, (NH₂)₂BuPPAOH, (NH₂)₂PPAI, HOBuPPG, minorgroove binder, fluorophore, quencher and a chemilumenescer.

Alternatively the T_(m)s of multiple modified oligonucleotides aresubstantially leveled for containing the same number of bases plus orminus 1 or 2 bases, with a T_(m) range of about ±2° C.

In some instances, modified bases are used that improve duplex stabilityin addition to those modified bases that decrease duplex stability.Modified bases that decrease duplex stability are well known, e.g.7-deazaadenine and 7-deazaguanine.

Use of Modified Oligonucleotides

The modified oligonucleotides of the present invention provides numerousadvantages over unmodified oligonucleotides, including superior mismatchdiscrimination. The modified oligonucleotides of the invention areparticularly useful as probes, wherein their hybridization to a targetsequence is detected, or as primers, wherein their hybridization to atarget sequence is followed by polynucleotide synthesis initiated fromthe 3′ terminus of the modified oligonucleotide, and the synthesizedproduct (i.e., the extension product) is detected.

The modified oligonucleotides of the present invention are useful inother techniques in which hybridization of an oligonucleotide to anothernucleic acid is involved. These include, but are not limited to,techniques in which hybridization of an oligonucleotide to a targetnucleic acid is the endpoint; techniques in which hybridization of oneor more oligonucleotides to a target nucleic acid precedes one or morepolymerase-mediated elongation on steps which use the oligonucleotide asa primer and the target nucleic acid as a template; techniques in whichhybridization of an oligonucleotide to a target nucleic acid is used toblock extension of another primer; techniques in which hybridization ofan oligonucleotide to a target nucleic acid is followed by hydrolysis ofthe oligonucleotide to release an attached label; and techniques inwhich two or more oligonucleotides are hybridized to a target nucleicacid and interactions between the multiple oligonucleotides aremeasured. Conditions for hybridization of oligonucleotides, and factorswhich influence the degree and specificity of hybridization, such astemperature, ionic strength and solvent composition, are well-known tothose of skill in the art. See, for example, Sambrook et al., supra;Ausubel, et al., supra; M. A. Innis et al. (eds.) PCR Protocols,Academic Press, San Diego, 1990; B. D. Hames et al. (eds.) Nucleic AcidHybridisation: A Practical Approach, IRL Press, Oxford, 1985; and vanNess et al. (1991) Nucleic Acids Res. 19:5143-5151.

Hybridization of probes and/or primers to target sequences proceedsaccording to well-known and art-recognized base-pairing properties, suchthat adenine base-pairs with thymine or uracil, and guanine base-pairswith cytosine. The property of a nucleotide that allows it to base-pairwith a second nucleotide is called complementarity. Thus, adenine iscomplementary to both thymine and uracil, and vice versa; similarly,guanine is complementary to cytosine and vice versa. An oligonucleotidewhich is complementary along its entire length with a target sequence issaid to be perfectly complementary, perfectly matched, or fullycomplementary to the target sequence, and vice versa. An oligonucleotideand its target sequence can have related sequences, wherein the majorityof bases in the two sequences are complementary, but one or more basesare noncomplementary, or mismatched. In such a case, the sequences canbe said to be substantially complementary to one another. If thesequences of an oligonucleotide and a target sequence are such that theyare complementary at all nucleotide positions except one, theoligonucleotide and the target sequence have a single nucleotidemismatch with respect to each other.

The modified pyrazolo[3,4-d]pyrimidine nucleotides of the inventionretain the base-pairing specificity of their naturally-occurringanalogues; PPPG analogues are complementary to cytosine, while PPPAanalogues are complementary to thymine and uracil. The PPPG and PPPAanalogues not only have a reduced tendency for so-called “wobble”pairing with non-complementary bases, compared to guanine and adenine,but the 3-substituted groups increase binding affinity in duplexes.Similarly, modified pyrimidines hybridize specifically to theirnaturally occurring counter partners.

Conditions for hybridization are well-known to those of skill in the artand can be varied within relatively wide limits. Hybridizationstringency refers to the degree to which hybridization conditionsdisfavor the formation of hybrids containing mismatched nucleotides,thereby promoting the formation of perfectly matched hybrids or hybridscontaining fewer mismatches; with higher stringency correlated with alower tolerance for mismatched hybrids. Factors that affect thestringency of hybridization include, but are not limited to,temperature, pH, ionic strength, concentration of organic solvents suchas formamide and dimethylsulfoxide and chaotropes. As is well known tothose of skill in the art, hybridization stringency is increased byhigher temperatures, lower ionic strengths, and lower solventconcentrations. See, for example, Ausubel et al., supra; Sambrook etal., supra; M. A. Innis et al. (eds.) PCR Protocols, Academic Press, SanDiego, 1990; B. D. Hames et al. (eds.) Nucleic Acid Hybridisation: APractical Approach, IRL Press, Oxford, 1985; and van Ness et al., (1991)Nucleic Acids Res. 19:5143-5151.

Thus, in the formation of hybrids (duplexes) between an oligonucleotideand its target sequence, the oligonucleotide is incubated in solution,together with a polynucleotide containing the target sequence, underconditions of temperature, ionic strength, pH, etc, that are favorableto hybridization, i.e., under hybridization conditions. Hybridizationconditions are chosen, in some circumstances, to favor hybridizationbetween two nucleic acids having perfectly-matched sequences, ascompared to a pair of nucleic acids having one or more mismatches in thehybridizing sequence. In other circumstances, hybridization conditionsare chosen to allow hybridization between mismatched sequences, favoringhybridization between nucleic acids having fewer mismatches.

The degree of hybridization of an oligonucleotide to a target sequence,also known as hybridization strength, is determined by methods that arewell-known in the art. A preferred method is to determine the T_(m) ofthe hybrid duplex. This is accomplished, as described supra; bysubjecting a duplex in solution to gradually increasing temperature andmonitoring the denaturation of the duplex, for example, by absorbance ofultraviolet light, which increases with the unstacking of base pairsthat accompanies denaturation. T_(m) is generally defined as thetemperature midpoint of the transition in ultraviolet absorbance thataccompanies denaturation. Alternatively, if T_(m)s are known, ahybridization temperature (at fixed ionic strength, pH and solventconcentration) can be chosen that it is below the T_(m) of the desiredduplex and above the T_(m) of an undesired duplex. In this case,determination of the degree of hybridization is accomplished simply bytesting for the presence of hybridized probe.

If a probe comprises a detectable label, assays for hybridized probe areusually designed to detect the presence of label in duplex material.This can be accomplished, for example, by specifically selecting duplexmaterial, specifically destroying single-stranded material, or utilizingsome combination of these methods. For example, hybridization reactionmixtures can be subjected to high-stringency conditions and/or singlestrand-specific nucleases; or duplexes can be purified by affinitytechniques specific for double-stranded, as opposed to single-stranded,nucleic acids. In a preferred embodiment of the invention, duplexes aredetected by release of label from a probe under conditions in whichlabel is released only when the probe is in a duplex. Another embodimentrequires the seperation of the label and quenchers when hybridized tothe target.

Detectable labels or tags suitable for use with nucleic acid probes arewell-known to those of skill in the art and include, but are not limitedto, radioactive isotopes, chromophores, fluorophores, chemiluminescentand electrochemiluminescent agents, magnetic labels, microspheres,colloidal metal (Taton et al, Science 289:1757-1760 (2000)), immunologiclabels, ligands and enzymatic labels. Suitable labels also include masslabels and those used in deconvolution of combinatorial chemistrylibraries, for example, tags that can be recognized by high performanceliquid chromatography (HPLC), gas chromatography, mass spectrometry,optical imaging fibers, surface plasmon resonance, correlationspectroscopy, nanotechnology (Guetence et al, J. Chromatogr. B. Biomed.Sci. Appl. 739:139-150 (2000)) and the like.

Methods for labeling of oligonucleotides are well-known to those ofskill in the art and include, for example, chemical and enzymaticmethods. By way of example, methods for incorporation of reactivechemical groups into oligonucleotides, at specific sites, are well-knownto those of skill in the art. Oligonucleotides containing a reactivechemical group, located at a specific site, can be combined with a labelattached to a complementary reactive group (e.g., an oligonucleotidecontaining a nucleophilic reactive group can be reacted with a labelattached to an electrophilic reactive group) to couple a label to aprobe by chemical techniques. Exemplary labels and methods forattachment of a label to an oligonucleotide are described, for example,in U.S. Pat. Nos. 5,824,796; 5,210,015; Kessler (ed.), NonradioactiveLabeling and Detection of Biomolecules, Springer-Verlag, Berlin, 1992;Kricka (ed.) Nonisotopic DNA Probe Techniques, Academic Press, SanDiego, 1992; Howard (ed.) Methods in Nonradioactive Detection, Appleton& Lange, Norwalk, 1993. Non-specific chemical labeling of anoligonucleotide can be achieved by combining the oligonucleotide with achemical that reacts, for example, with a particular functional group ofa nucleotide base, and simultaneously or subsequently reacting theoligonucleotide with a label. See, for example, Draper et al. (1980)Biochemistry 19:1774-1781. Enzymatic incorporation of label into anoligonucleotide can be achieved by conducting enzymatic modification orpolymerization of an oligonucleotide using labeled precursors, or byenzymatically adding label to an already-existing oligonucleotide. See,for example, U.S. Pat. No. 5,449,767. Examples of modifying enzymesinclude, but are not limited to, DNA polymerases, reversetranscriptases, RNA polymerases, etc. Examples of enzymes which are ableto add label to an already-existing oligonucleotide include, but are notlimited to, kinases, terminal transferases, ligases, glycosylases, etc.

If an oligonucleotide is capable of acting as a primer, the degree ofhybridization of the oligonucleotide can also be determined by measuringthe levels of the extension product of the primer. In the case, eitherthe primer can be labeled, or one or more of the precursors forpolymerization (normally nucleoside triphosphates) can be labeled.Extension product can be detected, for example, by size (e.g., gelelectrophoresis), affinity methods, or any other technique known tothose of skill in the art.

Primer extension (“minisequencing”, “genetic bit analysis”) assays arecommonly used for SNP typing and have the potential to be used in othergenotyping and mutation screening applications (Pastinen T. et al.,Genome Res., 10:1031-42 (2000)). In certain embodiments modified basesand minor groove binders improve primer extension assays in severalways. The added duplex stability provided by MGB, or 5-substitutedpyrimidine or 3-substituted pyrazolo[3,4-d]pyrimidine enables extensionsto be performed at elevated temperatures. This is advantageous becauseproblematic secondary structures in target molecules are eliminated atelevated temperatures. Also, hybridization of target to primer is fasterat higher temperature. Thermostable polymerases such as Taq polymeraseand Bst DNA polymerase may be used in such reactions.

Furthermore, MGBs and modified bases improve the specificity of assaysby eliminating one class of false postitive signals. Primer sequencesthat form hairpin structures or homodimers are prone totemplate-independent extension (the 5′ end of the primer functions astemplate), resulting in false positive signal. MGBs and modified baseson “templates” inhibit extension by DNA polymerases. Thus, MGBs on the5′ end, or modified bases on the 5′ end or middle of a primer, canprevent extension (false positives) from primer hairpins or primerdimers. Finally, PPG can be used to eliminate non-canonical structuresformed by G-rich oligonucleotides, enabling primer extension assays insuch sequences.

Other assays in which the present modified oligonucleotides areparticularly useful are described in co-pending application Ser. No.09/054,832.

Still other amplification assays in which modified oligonucleotides areuseful include the amplification assays based on the invasive cleavageof oligonucleotide probes by flap endonucleases (Lyamichev et al.,Nature Biotechnol., 17:292-296 (1999) and Olson, et al., High-ThroughputGene Expression Monitoring with the Invader® Assay, Poster, Society forBiomolecular Screening Conference, Vancouver, British Columbia, Canada,2000); self-sustained sequence replication type assays (Mueller et al,Histochem. Cell Biol., 108:431437 (1997)) and the like. Surprisingly,non-natural bases can be substituted in both the invader and genomicprobes of a cleavase-based assay. These modifications include but arenot limited to pyrazolo[3,4-d]pyrimidines, 3-substitutedpyrazolo[3,4-d]pyrimidines and 5-substituted pyrimidines. Non-naturalbackbones are also included such as monomers used in peptide nucleicacids, locked nucleic acids etc. Still further, the modifiedoligonucleotides can have attached minor groove binders, fluorophores,quenchers, and the like. One of skill in the art will appreciate thatchimeras can also be used to allow optimal enzyme activity andperformance.

In the present invention, marked improvements are unexpectedly shown incleavase-based assays, when modified bases were substituted for normalbases in both the invader and genomic probes. Thus, the use of themodified bases such as hydoxypropynylPPA (HOPPPA), (NH₂)₂PPPAOH and3-iododiaminoPPA allowed one to decrease the length of both the invaderand genomic probes, yet provide improved assay performance. In anotherembodiment non-natural bases are also incorporated in the cassetteprobe.

In view of the above, the present invention provides in one aspect, amethod for distinguishing polynucleotides with related sequences, themethod comprising:

(a) contacting a modified oligonucleotide having a defined sequencecomprising at least one 3-substituted pyrazolo[3,4-d]pyrimidine or5-substituted pyrimidine in place of a purine or pyrimidine base with atleast two polynucleotides, wherein one of the polynucleotides has atarget sequence that is perfectly complementary to the modifiedoligonucleotide and at least one of the other polynucleotides has atarget sequence with at least one base mismatch; and

(b) determining the degree of hybridization between the modifiedoligonucleotide and each of the polynucleotides.

Preferably, at least one of the other polynucleotides has a targetsequence with one or two base mismatches, more preferably only one basemismatch.

As noted above, a target sequence refers to a nucleotide sequence whichcomprises a site of hybridization for a probe or a primer. Targetsequences can be found in any nucleic acid including, but not limitedto, genomic DNA, cDNA, RNA and any amplified product thereof, and cancomprise a wild-type gene sequence, a mutant gene sequence, a non-codingsequence, a regulatory sequence, etc. A target sequence will generallybe less than 100 nucleotides, preferably less than 50 nucleotides, andmost preferably, less than 21 nucleotides in length.

The modified oligonucleotides used in this aspect of the invention areessentially modified probes and the polynucleotides can be distinguishedby determining which polynucleotides hybridizes to the modified probe.The modified probes can be labeled with any detectable label, or theprobe can have the capacity to become labeled either before or afterhybridization, such as by containing a reactive group capable ofassociation with a label or by being capable of hybridizing to asecondary labeled probe, either before or after hybridization to thetarget. Conditions for hybridization of nucleic acid probes arewell-known to those of skill in the art. See, for example, Sambrook etal., supra; Ausubel et al., supra; Innis et al., supra; Hames et al.supra; and van Ness et al., supra.

Hybridization can be assayed (i.e., hybridized nucleic acids can beidentified) by distinguishing hybridized probe from free probe by one ofseveral methods that are well-known to those of skill in the art. Theseinclude, but are not limited to, attachment of target nucleic acid to asolid support, either directly or indirectly (by hybridization to asecond, support-bound probe or interaction between surface-bound andprobe-conjugated ligands) followed by direct or indirect hybridizationwith probe, and washing to remove unhybridized probe; determination ofnuclease resistance; buoyant density determination; affinity methodsspecific for nucleic acid duplexes (e.g., hydroxyapatitechromatography); interactions between multiple probes hybridized to thesame target nucleic acid; etc. See, for example, Falkow et al., U.S.Pat. No. 4,358,535; Urdea et al., U.S. Pat. Nos. 4,868,105 and5,124,246; Freifelder, Physical Biochemistry, Second Edition, W. H.Freeman & Co., San Francisco, 1982; Sambrook, et al., supra; Ausubel etal., supra; Hames et al., supra; and other related references. Theduplex-stabilizing capability of MGB-modified oligonucleotide conjugatesmakes hybridization possible under more stringent conditions, whereinpotentially occluding secondary structure in the target nucleic acid canbe minimized. Accordingly, such MGB-modified oligonucleotides areparticularly preferred in this aspect of the invention.

In a related aspect, the present invention provides a method fordetecting the presence of a target sequence in a polynucleotide, themethod comprising:

(a) incubating a polynucleotide to be tested for the presence of thetarget sequence with a modified oligonucleotide having a sequence thatis substantially complementary to the target sequence underhybridization conditions; and

(b) identifying hybridized nucleic acids;

wherein the modified oligonucleotide comprises at least one3-substituted pyrazolo[3,4-d]pyrimidine in place of a purine residue.

Preferably, the modified oligonucleotide is a labeled probe and has atleast two 3-substituted pyrazolo[3,4-d]pyrimidine bases. In this groupof embodiments, a labeled probe is hybridized to a target and/or anextension product of a target, and a change in the physical state of thelabel is effected as a consequence of hybridization. As used herein, a“probe” is a nucleic acid molecule that is capable of hybridizing to atarget sequence in a second nucleic acid molecule. By way of example,one assay of this type, the hydrolyzable probe assay, takes advantage ofthe fact that many polymerizing enzymes, such as DNA polymerases,possess intrinsic 5′-3′ exonucleolytic activities. Accordingly, if aprobe is hybridized to a sequence that can serve as a template forpolymerization (for instance, if a probe is hybridized to a region ofDNA located between two amplification primers, during the course of anamplification reaction), a polymerizing enzyme that has initiatedpolymerization at an upstream amplification primer is capable ofexonucleolytically digesting the probe. Any label attached to such aprobe will be released, if the probe is hybridized to its target and ifamplification is occurring across the region to which the probe ishybridized. Released label is separated from labeled probe and detectedby methods well-known to those of skill in the art, depending on thenature of the label. For example, radioactively labeled fragments can beseparated by thin-layer chromatography and detected by autoradiography;while fluorescently-labeled fragments can be detected by irradiation atthe appropriate excitation wavelengths with observation at theappropriate emission wavelengths. See, e.g., U.S. Pat. No. 5,210,015.

In a variation of this technique, a probe contains both a fluorescentlabel and a quenching agent, which quenches the fluorescence emission ofthe fluorescent label. In this case, the fluorescent label is notdetectable until its spatial relationship to the quenching agent hasbeen altered, for example by exonucleolytic release of the fluorescentlabel from the probe. Thus, prior to hybridization to its targetsequence, the dual fluorophore/quencher labeled probe does not emitfluorescence. Subsequent to hybridization of thefluorophore/quencher-labeled probe to its target, it becomes a substratefor the exonucleolytic activity of a polymerizing enzyme which hasinitiated polymerization at an upstream primer. Exonucleolyticdegradation of the probe releases the fluorescent label from the probe,and hence from the vicinity of the quenching agent, allowing detectionof a fluorescent signal upon irradiation at the appropriate excitationwavelengths. This method has the advantage that released label does nothave to be separated from intact probe. Multiplex approaches utilizemultiple probes, each of which is complementary to a different targetsequence and carries a distinguishable label, allowing the assay ofseveral target sequences simultaneously.

The use of MGB-modified oligonucleotide conjugates in this and relatedmethods allows greater speed, sensitivity and discriminatory power to beapplied to these assays. In particular, the enhanced ability ofMGB-modified oligonucleotide conjugates to allow discrimination betweena perfect hybrid and a hybrid containing a single-base mismatch willfacilitate the use of hydrolyzable probe assays in the identification ofsingle-nucleotide polymorphisms and the like. One of skill in the artwill appreciate that compositions and methods, such as those of theinvention, that are capable of discriminating single-nucleotidemismatches will also be capable of discriminating between sequences thathave 2, 3, 4, 5, or even 6 or more mismatches with respect to oneanother.

In yet another related aspect, the present invention provides a methodfor primer extension, the method comprising incubating a polynucleotidecontaining a target sequence with one or more oligonucleotide primerscomplementary to the target sequence, in the presence of a polymerizingenzyme and nucleotide substrates under conditions favorable forpolymerization; wherein at least one of the oligonucleotide primerscontains a 3-substituted pyrazolo[3,4-d]pyrimidine or a 5-substitutedpyrimidine base in place of a purine or pyrimidine base.

Amplification procedures are those in which many copies of a targetnucleic acid sequence are generated, usually in an exponential fashion,by sequential polymerization and/or ligation reactions. In addition tothe more traditional amplification reactions discussed below, thepresent invention is useful in amplifications involving three-wayjunctures (see, WO 99/37085), signal amplification (see Capaldi, et al.,Nuc. Acids Res., 28:E21 (2000)), T7 polymerases, reverse transcriptase,RNase H, RT-PCR, Rolling Circles, cleavase and the like.

Many amplification reactions, such as PCR, utilize reiterativeprimer-dependent polymerization reactions. A primer is a nucleic acidthat is capable of hybridizing to a second, template nucleic acid andthat, once hybridized, is capable of being extended by a polymerizingenzyme (in the presence of nucleotide substrates), using the secondnucleic acid as a template. Polymerizing enzymes include, but are notlimited to, DNA and RNA polymerases and reverse transcriptases, etc.Conditions favorable for polymerization by different polymerizingenzymes are well-known to those of skill in the art. See, for example,Sambrook et al., supra; Ausubel, et al., supra; Innis et al., supra.Generally, in order to be extendible by a polymerizing enzyme, a primermust have an unblocked 3′-end, preferably a free 3′ hydroxyl group. Theproduct of an amplification reaction is an extended primer, wherein theprimer has been extended by a polymerizing enzyme.

Thus, in one embodiment of the invention, the methods and compositionsdisclosed and claimed herein are useful in improved amplificationreactions such as PCR. See, e.g., U.S. Pat. Nos. 4,683,202; 4,683,195and 4,800,159; Mullis and Faloona, supra; and Saiki et al., supra. Thepolymerization step of PCR is most often catalyzed by a thermostablepolymerizing enzyme, such as a DNA polymerase isolated from athermophilic bacterium, because of the elevated temperatures requiredfor the denaturation step of PCR. As discussed supra, one of theproblems heretofore associated with the practice of PCR is therequirement for relatively long oligonucleotide primers, havingsufficient hybrid stability to serve as primers at the elevatedtemperatures under which PCR is conducted. Modified oligonucleotides andespecially MGB-modified oligonucleotide conjugates are useful as primersin amplification reactions such as PCR, as the modified bases and MGBsincrease hybrid stability, thereby significantly extending the lowerlimit of useful primer length. In addition, MGB-modified oligonucleotideconjugates are useful in specialized PCR protocols wherein reducedprimer length is desirable. These include, but are not limited to,differential display, in which optimal primer length is below 10nucleotides, random amplification of polymorphism in DNA (RAPD)techniques, and amplification length polymorphism analyses. Liang et al,supra; Williams et al., supra.

The modified oligonucleotides of the present invention are applicable toany type of assay or procedure in which PCR or a related amplificationtechnique is used, including, but not limited to, hydrolyzable probeassays, priming with allele-specific oligonucleotides (ASOs), fragmentlength polymorphism analysis, single nucleotide polymorphism (SNP)analysis and microsatellite analysis, for example. These and othertechniques are useful in gene mapping, in the identification andscreening of disease-related genes, and in pharmacogenetics, to namejust a few applications.

In still another related aspect, the present invention provides a methodfor determining the nucleotide sequence of a polynucleotide, the methodcomprising:

(a) incubating the polynucleotide with a modified oligonucleotide arrayunder hybridization conditions; and

(b) determining to which of the modified oligonucleotides in the arraythe polynucleotide hybridizes;

wherein the modified oligonucleotides comprise at least one3-substituted pyrazolo[3,4-d]pyrimidine in place of a purine base.

In these procedures, an ordered array comprising a plurality of modifiedoligonucleotides of different known sequences is used as a platform forhybridization to one or more test polynucleotides, nucleic acids ornucleic acid populations. Determination of the oligonucleotides whichare hybridized and alignment of their known sequences allowsreconstruction of the sequence of the test polynucleotide. See, forexample, U.S. Pat. Nos. 5,492,806; 5,525,464; 5,556,752; and PCTPublications WO 92/10588 and WO 96/17957. Materials for construction ofarrays include, but are not limited to, nitrocellulose, glass, siliconwafers, optical fibers and other materials suitable for construction ofarrays such as are known to those of skill in the art.

A major problem with current array-based sequencing and analysis methodsis that the different oligonucleotides in an array will each have adifferent T_(m). Hence, it is difficult to determine the stringencyconditions that will provide maximum sensitivity, while retaining theability to distinguish single-base mismatches. This is a particularlyimportant consideration for most, if not all, applications of arraytechnology. Use of modified oligonucleotides and/or MGB-modifiedoligonucleotide conjugates in array-based sequencing and analysistechniques provides a solution to this problem. Surprisingly,conjugation of a MGB to a modified oligonucleotide makes its T_(m)relatively independent of base composition. Thus, for a population ofmodified oligonucleotides and MGB-modified oligonucleotide conjugates ofa given length, the T_(m) for a perfect hybrid falls within a relativelynarrow temperature range regardless of sequence. At the same time, theT_(m) for a single nucleotide mismatch is well below the T_(m) of theperfect match. Thus, arrays designed such that all modifiedoligonucleotides are the same length and are optionally present as theirMGB conjugates exhibit minimal variation in T_(m) among the differentoligonucleotides in the array, enabling more uniform hybridizationconditions for the entire array. A further advantage to the use ofmodified oligonucleotides and MGB-modified oligonucleotide conjugates inthese techniques is that it provides greater sensitivity, by allowingthe use of shorter oligonucleotides, at higher temperatures (and hencehigher stringency), while retaining single-nucleotide resolution.

An additional application of the present invention to array technologyis in the examination of patterns of gene expression in a particularcell or tissue (see, generally, Eisen, et al., METHODS IN ENZYMOLOGY,303:179-205 (1999)). In this case, modified oligonucleotides orpolynucleotides corresponding to different genes are arrayed on asurface, and a nucleic acid sample from a particular cell or tissuetype, for example, is incubated with the array under hybridizationconditions. Detection of the sites on the array at which hybridizationoccurs allows one to determine which modified oligonucleotides havehybridized, and hence which genes are active in the particular cell ortissue from which the sample was derived.

Array methods can also be used for identification of mutations orpolymorphisms, where wild-type and mutant sequences are placed in anordered array on a surface (see, Hacia, et al., J. Mol. Genet.,36:730-736 (1999)). Hybridization of a polynucleotide sample to thearray under stringent conditions, and determination of whicholigonucleotides in the array hybridize to the polynucleotide, allowsdetermination of whether the polynucleotide possesses the wild-type orthe mutant sequence. The increased discriminatory abilities ofMGB-oligonucleotide conjugates are especially useful in this applicationof array technology.

Accordingly, the present invention provides a method for identifying amutation in a target sequence of a gene of interest, the methodcomprising:

(a) incubating a polynucleotide comprising the target sequence with anarray of oligonucleotides of different sequences, wherein the differentsequences include the wild-type target sequence and different mutanttarget sequences, under hybridization conditions; and

(b) determining which of the oligonucleotides in the array becomehybridized to the polynucleotide;

wherein one or more purine residues in a plurality of theoligonucleotides are replaced with a 3-substitutedpyrazolo[3,4-d]pyrimidine.

In yet another related aspect, the present invention provides a methoddetermining the nucleotide sequence of a target sequence in apolynucleotide, the method comprising:

(a) contacting a polynucleotide comprising the target sequence with atleast two oligonucleotides of known sequence wherein one or more purineresidues of the oligonucleotides are replaced by a 3-substitutedpyrazolo[3,4-d]pyrimidine, and wherein one of the at least twooligonucleotides has a sequence that is perfectly complementary to thetarget sequence and at least one other of the oligonucleotides has arelated target sequence and incubating each of the oligonucleotides withthe polynucleotide under hybridization conditions; and

(b) determining the degree of hybridization between each of theoligonucleotides and the polynucleotide.

In one embodiment, a collection of all possible n-mer oligonucleotides(where n is an integer less than about 10) are used in a hydrolyzableprobe assay to determine a nucleotide sequence. Each oligonucleotide isuniquely labeled (and preferably modified) and analysis of releasedlabel indicates which of the oligonucleotides has hybridized to thetarget sequence. Alignment of the sequences of the oligonucleotideswhich have hybridized provides the nucleotide sequence.

Modified oligonucleotides, and more preferably modifiedoligonucleotide-MGB conjugates are also useful in primer-dependentmethods of DNA sequencing, such as the chain-termination method and itsderivatives, originally described by Sanger et al., supra. Use ofMGB-modified oligonucleotide conjugates in chain-termination sequencingallows the use of shorter primers at higher stringency, and enables agreater degree of mismatch discrimination during sequencing. Examplesinclude, but are not limited to, a search for genes sharing a shortregion of homology (on the order of a few amino acids) and sequencing ina region in which very little existing sequence information isavailable. MGB-oligonucleotide conjugates are useful in such shortprimer sequencing techniques.

In still another embodiment, the present invention provides a method forexamining gene expression in a cell, the method comprising:

(a) incubating a population of polynucleotides representative of thegenes expressed in the cell with an oligonucleotide array comprising aplurality of modified oligonucleotides of different sequences underhybridization conditions, and

(b) determining which of the modified oligonucleotides in the arraybecome hybridized to polynucleotides;

wherein said modified oligonucleotides comprise at least one3-substituted pyrazolo[3,4-d]pyrimidine in place of a purine.

In one group of embodiments, the method is carried out with a pluralityof expressed genes from multiple cell-types or tissues. The genes arepreferably labeled with different detection labels, then hybridized toan array at the same time and monitored via the label to determine eachgene's expression pattern.

In addition to the assays and diagnostic methods described above, themodified oligonucleotides and modified bases described herein will haveutility in antisense technologies. Antisense oligonucleotides are knownto selectively inhibit gene expression and provide a genetic approachfor disease treatment and prevention (Smith et al, Int. J. Oncol.,17:841-850 (2000)). Other modified oligonucleotides have been used toimprove the performance of antisense oligonucleotides (Zhang et al, Nat.Biotechnol., 18:862-867 (2000); Flanagan et al, Nat. Biotechnol.,14:1139-1145 (1996)). Accordingly, another embodiment of the presentinvention is the use of the 5-substituted pyrimidines, unsubstitutedpyrazolo[3,4-d]pyrimidines and 3-substituted pyrazolo[3,4-d]pyrimidineas monomers, either alone or in any combination, in the synthesis ofantisense oligomers. In another embodiment the modified bases describedherein can be used as monomers in an oligonucleotide to decreaseenzymatic degradation of the antisense oligomers.

New Modified Bases

In another aspect, the present invention provides a number of newmodified bases. These bases have the general formula:

wherein Z¹ is a member selected from the group consisting of H, F andOR^(a) wherein R^(a) is a member selected from the group consisting ofH, (C₁-C₈)alkyl and a hydroxy protecting group; Z² is a member selectedfrom the group of H, (C₁-C₈)alkyl, or is optionally combined with Z¹ toform a five- to seven-membered ring, having from one to threeheteroatoms selected from the group consisting of O, S and N; Y¹ is amember selected from the group consisting of OH, a protected hydroxygroup and O—P¹, wherein P¹ is a phosphoramidite or H-phosphonate group;Y² is a member selected from the group consisting of OH, a protectedhydroxy group and O—P², wherein p² is a phosphoramidite, H-phosphonate,monophosphate, diphosphate or triphosphate; and B is a modifiednucleotide selected from the group consisting of:

wherein X¹¹ and X¹² are each independently selected from the groupconsisting of H, NH₂ and a protected amino group; each R¹¹ isindependently selected from the group consisting of protected orunprotected forms of 3-hydroxyprop-1-ynyl, 3-aminoprop-1-ynyl,3-methoxyprop-1-ynyl, 4-hydroxy-1-butynyl, 4-amino-1-butynyl and3-(hydroxymethyl)-4-hydroxy-1-butynyl; and each R¹² is independentlyselected from the group consisting of heterocyclyl(C₁-C₁₂)alkyl,heterocyclyl(C₂-C₁₂)alkenyl, heterocyclyl(C₂-C₁₂)alkynyl, heterocyclyl,3-hydroxyprop-1-ynyl, 3-aminoprop-1-ynyl, 3-methoxyprop-1-ynyl,4-hydroxy-1-butynyl, 4-amino-1-butynyl and3-(hydroxymethyl)-4-hydroxy-1-butynyl, with the proviso that R¹² isother than 2-pyridylethynyl.

In one group of embodiments, B is

Preferably, X¹¹ is NH₂ and X¹² is H. More preferably, X¹¹ is NH₂, X¹² isH, Y¹ is O—P¹, Y² is a protected hydroxy, Z¹ is H, and R¹² is selectedfrom 3-hydroxyprop-1-ynyl, 3-aminoprop-1-ynyl, 4-hydroxy-1-butynyl,4-amino-1-butynyl, 3-(hydroxymethyl)-4-hydroxy-1-butynyl,3-methoxyprop-1-ynyl, 2-furanyl, 3-furanyl, 2-thienyl, 3-thienyl,2-pyrrolyl, 3-pyrrolyl, 1,3-isoxazol-4-yl, 1,3-isoxazol-5-yl,1,3-isoxazol-2-yl, 2-imidazolyl, 4-imidazolyl, 2-pyridyl, 3-pyridyl and4-pyridyl. In particularly preferred embodiments, Y¹ is—O—[(2-cyanoethyl) N,N-diisopropylphosphoramidite] and Y² is—O-(4,4′-dimethoxytrityl).

In another group of embodiments, B is

Preferably, X¹² is NH₂ or H. More preferably, X¹² is NH₂ or H, Y¹ isO—P¹, Y² is a prot hydroxy, Z¹ is H, and R¹² is selected from3-hydroxyprop-1-ynyl, 3-aminoprop-1-ynyl, 3-(hydroxymethyl)4-hydroxy-1-butynyl, 3-methoxyprop-1-ynyl, 2-furanyl, 3-furanyl,2-thienyl, 3-thienyl, 2-pyrrolyl, 3-pyrrolyl, 1,3-isoxazol-4-yl,1,3-isoxazol-5-yl, 1,3-isoxazol-2-yl, 2-imidazolyl, 4-imidazolyl,2-pyridyl, 3-pyridyl and 4-pyridyl. In particularly preferredembodiments, Y¹ is —O—[(2-cyanoethyl) N,N-diisopropylphosphoramidite]and Y² is —O-(4,4′-dimethoxytrityl).

In still other preferred embodiments, the modified oligonucleotides ofthe invention have at least one base of formula III (including those inwhich the acetyl protecting groups are removed, and including otherprotected forms and activated forms thereof).

Preparation of compounds of formula III (including compounds wherein the6-amino group is protected and the hydroxy groups of the sugar areeither protected or activated as a phosphoramidite) are provided inReaction Scheme 6, above.

In the most preferred embodiments of the invention, the modified basesare selected from formulae IVa, IVb or IVc.

These compounds are particularly well-suited for use in automaticoligonucleotide synthesizers, and in preparing certain modifiedoligonucleotides described herein.

Other modified bases that are useful in the present invention includethose represented by formulae Va and Vb:

wherein R⁷ is selected from OH, SH or NH₂. These compounds can besynthesized by methods described herein.

In another group of embodiments, B is

Preferably, X¹¹ is NH₂. More preferably, X¹¹ is NH₂, Y¹ is —O—P¹, Y² isa protected Z¹ is H, and R¹¹ is selected from 3-hydroxyprop-1-ynyl,3-aminoprop-1-ynyl, 4-hydroxy-1-butynyl. 4-amino-1-butynyl,3-(hydroxymethyl)-4-hydroxy-1-butynyl, and 3-methoxyprop-1-ynyl. Inparticularly preferred embodiments, Y¹ is —O—[(2-cyanoethyl)N,N-diisopropylphosphoramidite] and Y² is —O-(4,4′-dimethoxytrityl).

In another group of embodiments, B is

Preferably, Y¹ is O—P¹, Y² is a protected hydroxy, Z¹ is H, R¹¹ isselected from 3-hydroxyprop -1-ynyl, 3-aminoprop-1-ynyl,4-hydroxy-1-butynyl, 4-amino-1-butynyl, 3-(hydroxymethyl4-hydroxy-1-butynyl, and 3-methoxyprop-1-ynyl. In particularly preferredembodiments, Y¹ is —O—[(2-cyanoethyl) N,N-diisopropylphosphoramidite]and Y is —O-(4,4′-dimethoxytrityl).

In a related aspect, the present invention provides modifiedoligonucleotides having the formula:

wherein each Z¹ is independently selected from H, F and OR^(a) whereinR^(a) is a member selected from H, (C₁-C₈)alkyl and a hydroxy protectinggroup; each Z² is H or (C₁-C₈)alkyl, or is optionally combined with Z¹to form a five- to seven-membered ring; each Z³ is selected from O, S orNH; each Y is independently selected from P(O)OH, P(S)OH and P(O)CH₃;the subscript n is an integer of from 1 to 98; W¹ and W² are eachindependently selected from H, a monophosphate, a diphosphate, atriphosphate and a minor groove binder-linking group moiety having anoptionally attached reporter group or quencher; and each B isindependently selected from the group consisting of adenine, guanine,cytosine, uridine and modified bases of the formula:

wherein X¹¹ and X¹² are each independently selected from H, NH₂ and aprotected amino group; each R¹¹ is independently selected from protectedor unprotected forms of 3-hydroxyprop-1-ynyl, 3-aminoprop-1-ynyl,3-methoxyprop-1-ynyl, 4-hydroxy-1-butynyl, 4-amino-1-butynyl, and3-(hydroxymethyl)-4-hydroxy-1-butynyl; and each R¹² is independentlyselected from the group consisting of protected or unprotected forms of3-hydroxyprop-1-ynyl, 3-aminoprop-1-ynyl, 3-methoxyprop-1-ynyl,4-hydroxy-1-butynyl, 4-amino-1-butynyl,3-(hydroxymethyl)-4-hydroxy-1-butynyl, heterocyclyl(C₁-C₁₂)alkyl,heterocyclyl(C₂-C₁₂)alkenyl, heterocyclyl(C₂-C₁₂)alkynyl andheterocyclyl, with the provsio that R¹² is other than 2-pyridylethynyl;and

with the further proviso that at least one of the Bs is selected fromthe modified bases, and optionally, one or more of the Bs has anattached minor groove binder-linking group moiety, reporter group or acombination thereof.

Particularly preferred modified bases are those that have been describedabove.

EXAMPLES

In the hydrolyzable probe assay, a labeled probe is added to a PCRreaction. The probe is complementary to a region between the two PCRprimers and is labeled with two fluorophores, one of which quenches thefluorescence of the other. The probe is designed to hybridize to itscomplementary target sequence on one of the PCR product strands at orabove the strand extension temperature typically used in PCR (55-75°C.). The polymerizing enzymes normally used in PCR (Taq polymerase inparticular) possess an intrinsic 5′-exonuclease activity. Duringsynthesis of new strands in the extension stage of the PCR reaction,this 5′-exonuclease activity will act on complementary strands bound tothe template. If a probe, labeled as described above, is bound to thetemplate, the 5′-exonuclease activity associated with the polymerizingenzyme will liberate the bound fluorophore. Once liberated, itsfluorescence will no longer be quenched, and a fluorescent signal willbe obtained. See, for example, U.S. Pat. No. 5,210,015; Livak et al.(1995) PCR Meth. App. 4:357-362; and Heid et al. (1996) Genome Res.6:986-994.

Thin-layer chromatography was run on silica gel 60 F-254 (EM Reagents)aluminum-backed plates. ¹H NMR were obtained at 300 MHz on a VarianVXR-300 spectrometer. Two-dimensional (Cosy) and NOE experimentsassisted in the assignment of proton resonances. Elemental analyses wereperformed by Quantitative Technologies Inc. (Boundbrook, N.J.).

Example 1

This example illustrates the synthesis of5-(Prop-2-ynyl-4-methylbenzoate)-5′—O-(4,4′-dimethoxytriphenylmethyl)-2′-deoxyuridine3′-[(2-cyanoethyl) N,N-diisopropylphosphoramidite] (3).

5-(Prop-2-ynyl-4-methylbenzoate)-2′-deoxyuridine (1)

To a mixture of 5-iodo-2′-deoxyuridine (5.0 g, 14.12 mmol), CuI (270 mg,1.42 mmol), Pd(PPh₃)₄ (0.82 g, 0.714 mmol), and triethylamine (2.4 mL)in 30 mL of anhydrous DMF was added prop-2-ynyl 4-methylbenzoate (6.10g, 35.06 mmol). The mixture was stirred under argon for 4 h. and thenevaporated to dryness. The residue was triturated in methanol and theexcess prop-2-ynyl 4-methylbenzoate that precipitated was filtered away.The filtrate was evaporated and the residue was purified by silica gelchromatography eluting with 10% methanol in ethyl acetate. The pureproduct fractions were evaporated to dryness and the residue wasprecipitated from ethyl aceate-ether: 3.14 g (56%) yield; TLC (10%methanol in ethyl acetate), R_(f)=0.50; ¹H NMR (DMSO-d₆) δ 11.68 (1H, s,uracil N—H), 8.29 (1H, s, 6-H), 7.89 and 7.35 (4H, 2×d, J=8.2 Hz,toluoyl Hs), 6.10 (1H, t, J=6.4 Hz, 1′—H), 5.24 (1H, d, J=4.4 Hz,3′—OH), 5.15 (2H, s, alkynyl-CH₂), 5.12 (1H, t, J=5.2 Hz, 5′—OH), 4.24(1H, m, 3′-H), 3.79 (1H, q, 4′-H), 3.59 (2H, m, 5′-Hs), 2.39 (3H, s,toluoyl-CH₃), 2.13 (2H, m, 2′-H).

5-(Prop-2-ynyl-4-methylbenzoate)-5′-O-(4,4′-dimethoxytriphenylmethyl)-2′-deoxyuridine2.

To a solution of 1(3.0 g, 7.50 mmol) in 45 mL of anhydrous pyridine wasadded dimethoxytrityl chloride (3.0 g). The resulting solution wasstirred for 4 h. at room temperature and then poured into 400 mL of 5%sodium bicarbonate solution. The mixture was extracted with ethylacetate (2×300 mL) and the extract was dried over sodium sulfate,filtered and evaporated. The residue was purified by silica gelchromatography eluting with 5% methanol in the ethyl acetate. The pureproduct fractions were pooled and evaporated affording 2 as a foam: 4.16g (79%) yield

5-(Prop-2-ynyl-4-methylbenzoate)-5′-O-(4,4′-dimethoxytriphenylmethyl)-2′-deoxyuridine3[(2-cyanoethyl) N,N-diisopropylphosphoramidite] (3).

To a solution of 2 (4.0 g, 5.70 mmol) in 130 mL of anhydrous methylenechloride, containing 3.0 mL of N,N-diisopropylethylamine was addedchloro(2-cyanoethoxy)(N,N-diisopropylamino)phosphine (2.22 mL) underargon. The solution was stirred for 30 min at room temperature and thentreated with 3.0 mL of methanol. The solution was diluted with 300 mL ofethyl acetate and washed with 300 mL of 5% sodium bicarbonate solution.The aqueous phase was extracted with 300 mL of ethyl acetate and thecombined organic phases were dried over sodium sulfate, filtered andevaporated. The residue was purified by silica gel chromatographyeluting with a gradient of 30 to 0% hexane in ethyl acetate (2%triethylamine). The pure fractions were pooled and evaporated and theresidue was precipitated from ethyl acetate-hexanes: 3.35 g (65%) yield;TLC (20% hexane in ethyl acetate), R_(f)=0.82 and 0.71 (diasteromers);³¹P NMR (DMSO-d₆) δ 147.82 and 147.45.

Example 2 Phase 1 Preparation of(2R,5R)-5-(4-amino-3-iodopyrazolo[3,4-d]pyrimidinyl)-2-(hydroxymethyl)oxolan -3-ol (9) 3-Iodo-1,5-dihydropyrazolo[3,4-d]pyrimidin-4-one (4)

The synthesis of this compound was previously reported by Taylor et. al(Tetrahedron, 48(37):8089-8100 (1992)) using a N-iodosuccinimide. Oursynthesis, employing iodine momochloride as the iodinating agent isdescribed below.

To a 1.0 L solution of 1.2 M sodium acetate was added4-hydroxypyrazolo[3,4-d]pyrimidine (25 g, 184 mmol) followed by iodinemonochloride (46 g, 284 mmol). The mixture was stirred in a sealedcontainer for 4 h. at 110° C. The completed reaction was cooled to roomtemperature and treated with a solution of 30 g of sodium metabisulfitein 200 mL of water. The white precipitate that formed was filtered andrinsed with cold water. The solid was then dissolved in 200 mL of 3.2 Mpotassium hydroxide solution. Hydrazine monohydrate (5 mL) was added andthe solution was stirred for 15 min. The solution was then acidified toca. pH 7 by addition of 50 mL of concentrated HCl followed by a fine pHadjustment with acetic acid. The solid that formed was filtered, rinsedwith cold water and dried: 55.1 g (114% yield). Note—it is difficult toremove residual water by drying the solid under vacuum. The residualwater will be removed by a pyridine evaporation process in the nextstep.

3-Iodo-1,5-dihydropyrazolo[3,4-d]pyrimidin-4-thione (5)

Compound 4 (21.5 g, 82.1 mmol) was suspended in 150 mL of anhydrouspyridine and the mixture was evaporated to dryness. The solid wasre-suspended in 170 mL of dry pyridine (under argon) and P₂S₅ (26.8 g)was added. The mixture was stirred for 10 min at 65° C. and then for 2-6hours at 95° C. The resulting solution was cooled to room temperatureand degassed by bubbling a stream of argon into the solution (sulfidegas is passed into a trap containing sodium hydroxide solution). Thereaction solution was then reduced in volume until a thick syrup formed.Excess P₂S₅ was decomposed by addition of 1 mL aliquots of water, untilthe vigorous reaction ceased, followed by addition of 500 mL of waterand 10 mL of acetic acid. The mixture was warmed to 70° C. for 1 h toexpedite expulsion of hydrogen sulfide gas and then diluted with 500 mLof water and cooled in an ice-bath. The solid was filtered, washed withwater and dryed: 19.8 g (87%) yield.

4-Ethylthio-3-iodopyrazolo[3,4-d]pyrimidine (6)

Compound 5 (43.5 g, 157 mmol) was stirred in potassium hydroxidesolution (38.6 g KOH in 350 mL of water) for 30 min. The mixture wasfiltered and the filtrate was acidified to pH 10 by addition of aceticacid and then diluted with 350 mL of absolute ethanol. Iodoethane (10mL) was added and the solution was stirred at room temperature.Additional 10 mL aliquots of iodoethane were added after 30 min. and 1.0h. The reaction was complete after a total of 90 min. Other runsrequired further addition of iodoethane to complete the reaction. Thereaction solution was diluted with 700 mL of water and 20 mL of aceticacid. The mixture was cooled in an ice-bath and the solid was filtered,rinsed with water and dried. This crude product was dissolved in 300 ofDMF and stirred at 90° C. for 15 min. Insoluble material was filteredaway and the filtrate was diluted with 1 L of water and cooled in anice-water bath. The solid was filtered, rinsed with water and dried: 19g (40%) yield.

[(2R,5-R)-5-(4-Ethylthio-3-iodopyrazolo[3,4-d]pyrimidinyl)-3-(4-methylphenylcarbonyloxy)oxolan-2-yl]methyl4-methylbenzonate (7)

Compound 6 was converted to the corresponding potassium salt by reactionwith 1 molar equivalent of potassium hydroxide in water. The resultingsolution was evaporated to dryness and the residue was evaporated fromdry acetonitrile. The potassium salt of 6 (29.0 g, 94.73 mmol) wasdissolved in 80 mL of anhydrous DMF and then diluted with 830 mL ofanhydrous acetonitrile. The chlorosugar derivative (48 g, 123 mmol) wasadded in one portion and the mixture was stirred for 3 h and thendiluted with 1.5 L of 25% aqueous methanol. The mixture was allow to sitat 5° C. overnight. The crystals were filtered, rinsed with 25% aqueousmethanol and dried: 32.2 g (52%) yield.

(2R,5R)-2-(hydroxymethyl)-5-(3-iodo-4-methylpyrazolo[3,4-d]pyrimidinyl)oxolan-3-ol(8)

To a suspension of 7 (10.97 g, 16.66 mmol) in 250 mL of methanol wasadded 22 mL of 1N sodium methoxide in methanol. The mixture was stirredat reflux and the reaction progress was monitored as soon as the mixtureturned to a clear solution Note-formation of side products are observedif refluxing is continued after complete conversion to 5. The reactionwas quenched by addition of 1.34 mL of acetic acid as soon as onecomponent, corresponding to the desired product, is observed by TLC. Thesolution was evaporated and the residue was precipitated frommethanol-ether-hexane. The solid was filtered and dried: 6.8 g (104%)yield crude product (contains sodium acetate).

(2R,5R)-5-(4-amino-3-iodopyrazolo[3,4-d]pyrimidinyl)-2-(hydroxymethyl)oxolan-3-ol(9)

Compound 8 (6.8 g, 17.35 mmol) was stirred in 200 mL of concentratedammonium hydroxide (sealed container) at room temperature for 36 h. Themixture was evaporated and the residue was precipitated fromacetonitrile-ether. The solid was filtered and dried: 5.36 g (82%)yield. NMR and spectral data on this compound is identical to

Phase 2 Preparation of3-{4-((1E)-1-aza-2-methylprop-1-enyl)-1-((2R,5R)-5-{[Bis(4-methoxyphenyl)phenylmethoxy]methyl}-4-{[bis(methylethyl)amino](2-cyanoethoxy)phosphinooxy}oxolan-2-yl)pyrazolo[3,4-d]pyrimidin-3-yl]prop-2-ynyl4-methoxybenzoate (13; R1═—OCOPhCH₃)3-{1-{(2R,5R)-4-hydroxy-5-(hydroxymethyl)oxolan-2-yl]-4-aminopyrazolo[3,4-d3-yl}prop-2-ynyl}4-methylbenzoate (10; R¹=—OCOPhCH₃)

To a mixture of 9 (2.40 g, 6.37 mmol), CuI (124 mg, 0.648 mmol),Pd(PPh₃)₄ (380 mg, 0.331 mmol), and triethylamine (1.32 mL) in 12 mL ofanhydrous DMF was added prop-2-ynyl 4-methylbenzoate (1.87 g, 11.85mmol). The mixture was stirred under argon for 12 h. and then evaporatedto dryness. The residue was purified by silica gel chromatographyeluting with 5% methanol in ethyl acetate. The pure product fractionswere evaporated affording a foam: 2.29 g (85%) yield; TLC (10% methanolin ethyl acetate), R_(f)=0.43; ¹H NMR (DMSO-d₆) δ 8.26 (1H, s, 6-H),7.92 and 7.37 (4H, 2×d, J=8.5Hz, toluoyl-Hs), 6.55 (1H, t, J=6.3 Hz,1′-H), 5.29 (2H, s, alkynl-CH₂), 5.28 (1H, d, J=4.7Hz, 3′—OH), 4.76 (1H,t, J=5.7 Hz, 5′—OH), 4.41 (1H, m, 3′—H), 3.81 (1H, m, 4′-H), 3.49 and3.56 (2H, 2×m, 5′-Hs), 2.76 and 2.24 (2H, 2×m, 2′-Hs), 2.39 (3H, s,toluoyl-CH₃).

3-{4-((1E)-1-aza-2-methylprop-1-enyl)-1-((2R,5R)-4-hydroxy-5-(hydroxymethyl)oxolan-2-yl]pyrazolo[3,4-d]pyrimidin-3-yl}prop-2-ynyl 4-methylbenzoate (11;R¹=OCOPhCH₃)

Compound 10 (1.76 g, 4.16 mmol) was stirred in a solution of 5.0 mL ofN,N-dimethylacetamide, 1.9 mL of N,N-dimethylacetamide dimethyl acetaland 2.0 mL of anhydrous triethylamine for 15 h. at room temperature. Thesolvents were evaporated and the residue was evaporated twice fromxylenes affording 11 as a foam. TLC (10% methanol in ethyl acetate),R_(f)=0.29; ¹H NMR (DMSO-d₆) δ 8.51 (1H, s, 6-H), 7.90 and 7.37 (4H,2×d, J=8.3 Hz, toluoyl protons), 7.28, 7.14 and 6.74 (13H, d and 2 m,J=7.1 Hz for the doublet), trityl protons), 6.63 (1H, m, 1′—H), 5.32(1H, d, J=5.0 Hz, 3′—OH), 5.24(2H, s, alkynl-CH₂), 4.56 (1H, m, 3′-H),3.93 (1H, m, 4′-H), 3.68 (6H, s, methoxy Hs), 3.32 and 3.11 (6H, 2×s,N-methyls), 3.09-2.95 (2H, m, 5′-Hs), 2.81 and 2.32 (2H, 2×m, 2′-Hs),240 (3H, s, =-Me), 2.19 (3H, s, toluoyl-Me).

3-{4-((1E)-1-aza-2-methylprop-1-enyl)-1-((2R,5R)-5-{[Bis(4-methoxphenyl)phenylmethoxymethyl}-4-hydroxyoxolan-2-yl)pyrazolo[3,4-d]primidin-3-yl]prop-2-ynyl4-methylbenzoate (12; R¹=—OCOPhCH₃)

To a solution of 11 in 25 mL of anhydrous pyridine was addeddimethoxytrityl chloride (1.67 g). The resulting solution was stirredfor 4 h. at room temperature and then poured into 250 mL of 5% sodiumbicarbonate solution. The mixture was extracted with ethyl acetate andthe extract was dried over sodium sulfate, filtered and evaporated. Theresidue was purified by silica gel chromatography eluting with 5%methanol in the ethyl acetate. The pure product fractions were pooledand evaporated affording 12 as a foam: 2.06 g (62%) yield for thetwo-step process.

3-{4-((1E)-1-aza-2-methylprop-1-enyl)-1-((2R,5R)-5-{([Bis(4-methoxypheny)phenylmethoxy]methyl}-4-{[bis(methylethyl)amino](2-cyanoethoxy)phosphinooxy}oxolan-2-yl)pyrazolo[3,4-d]pyrimidin-3-yl]prop-2-ynyl4-methoxybenzoate (13; R¹═—OCOPhCH₃)

or,

1-[2-Deoxy-5-O-(4,4′-dimethoxytriphenylmethyl)-β-D-erythro-pentofuranosyl]-4-[(dimethylamino)prop-1-enyl]-3-(prop-2-ynyl-4-methylbenzoate)1H-pyrazolo[3,4-d]pyrimidine 3′-[(2-cyanoethyl)N,N-diisopropylphosphoramidite] (13)

To a solution of 12(2.03 g, 2.56 mmol) in 60 mL of anhydrous methylenechloride, containing 1.33 mL of N,N-diisopropylethylamine was addedchloro(2-cyanoethoxy)(N,N-diisopropylamino)phosphine (1.0 mL) underargon. The solution was stirred for 1.0 h at room temperature and thentreated with 2.0 mL of methanol. The solution was diluted with 250 mL ofethyl acetate and washed with 200 mL of 5% sodium bicarbonate solution.The organic phase was dried over sodium sulfate, filtered andevaporated. The residue was purified by silica gel chromatographyeluting with 2% triethylamine in ethyl acetate. The pure fractions werepooled and evaporated. The phosphoramidite (13) was precipitated fromether-hexanes: 1.82 g (71%) yield; TLC (5% methanol in ethyl acetate),R_(f)=0.32; ³¹P NMR (DMSO-d₆) δ 147.90 and 147.22.

Example 3

This example illustrates the preparation ofN-{3-[1-((2R,5R)-5{[bis(4-methoxyphenyl)phenylmethoxy]methyl}-4-{[bis(methylethyl)amino](2-cyanoethoxy)phosphinooxy}oxolan-2-yl)-6-amino-4-oxo(5-hydropyrazolo[3,4-d]pyrimidin-3-yl)]propyl}-2,2,2-trifluoroacet

3-Iodo-4-methoxypyrazolo[3,4-d]pyrimidine-6-ylamine(14)

4-Methoxy-pyrazolo[3,4-d]pyrimidin-6-ylamine (6.75 g, 40.87 mmol) wassuspended in an aqueous solution containing sodium acetate (6.0 g, 44.09mmol) and iodine monochloride (9.12 g, 56.17 mmol) and stirred at 100°C. in a sealed reaction vessel for 24 h. The resulting mixture wascooled to room temperature and treated with a solution of sodiummetabisulfite (3.6 g, 18.94 mmol) in 24 mL of water. The solid thatformed was filtered, rinsed with water and dried: 6.93 g (58%) yield;TLC (10% methanol in ethyl acetate), R_(f)=0.57; ¹H NMR (DMSO-d₆) δ13.08 (1H, br s, N-1 proton), 10.58 (1H, s, N-5 proton), 6.60 (2H, br s,6-amino).

[(2R,5R)-5-(6-Amino-3-Iodo-4-methoxypyrazolo[3,4-d]pyrimidinyl)-3-(4-methylphenylcarbonyloxy)oxolan-2-yl]methyl4-methylbenzoate (15)

To a suspension of (14) (6.68 g, 22.95 mmol) in 150 mL of methanol wasadded 8.05 mL of a 2.85 M methanolic potassium hydroxide. The mixturewas stirred for one minute and then diluted with 100 mL of toluene andevaporated. The solid potassium salt of 1 was dried under vacuum. Thepotassium salt was suspended in 75 mL of anhydrous DMF and then dilutedwith 420 mL of anhydrous acetonitrile.1-Chloro-1,2-dideoxy-3,5-di-O-toluoylribofuranose (8.95 g, 22.95 mmol)was immediately added and the reaction mixture was stirred at roomtemperature under argon for 1 h. and then filtered. The filtrate wasevaporated and the residual foam was recrystallized twice from methanol:6.59 g (45%) yield; TLC (1:1, ethyl acetate/hexane), R_(f)=0.52; ¹H NMR(DMSO-d₆) δ 7.93 and 7.37 (8H, m and d, J=7.9 Hz for the d, aromatic),7.10 (2H, br s, 6-amino), 6.51 (1H, t, J=6.6 Hz, 1′-H), 5.69 (1H, m,3′-H), 4.44 (3H, m, 4′- and 5′-Hs), 3.99 (3H, s, 4-methoxy), 3.19 and2.63 (2H, 2×m, 2′-Hs), 2.40 and 2.38 (6H, 2×s, toluoyl methyl protons).

[(2R,5R)-5-(6-Amino-3-Iodo-4-methoxypyrazolo[3,4-d]pyrimidinyl)-2-(hydroxymethyl)oxolan-3-ol(16)

To a suspension of 15 (32.4 g, 50.40 mmol) in 600 mL of methanol wasadded 12.5 mL of 1M sodium methoxide in methanol. The reaction mixturewas stirred at reflux for 18 h. and then cooled in a freezer (−10° C.).The crystals of 3 that formed were filtered and rinsed with ice-coldmethanol: 10.95 g yield. Acetic acid (12.5 mL) was added to the filtrateand the volume was reduced to about 300 mL. The solution was allowed tosit in the freezer overnight and another crop of crystals (3.95 g) wascollected. The filtrate was evaporated to dryness and the residual oilwas triturated in ether. The solid that formed was filtered, dried andrecrystallized from boiling water: 2.03 g. Total yield=16.93 g (83%);TLC (10% methanol in ethyl acetate), R_(f)=0.23; ¹H NMR (DMSO-d₆) δ 7.02(2H, br s, 6-amino), 6.33 (1H, t, J=6.1 Hz), 5.24 (1H, d, J=4.4 Hz,3′—OH), 4.73 (1H, t, J=5.6 Hz, 5′-OH), 4.36 (1H, m, 3′-H), 3.99 (3H, s,4-methoxy), 3.75 (1H, m, 4′-H), 3.51-3.32 (2H, m, 5′-Hs), 2.79 and 2.17(2H, 2×m, 2′-Hs). Anal. Calcd. For C₁₁H₁₄IN₅O₄.0.3H₂O; C, 32.02; H,3.57; N, 16.98. Found: C, 32.13; H, 3.35; N, 16.77.

1-[(2R,5R)-(5-hydroxymethyl)oxolan-2-yl]-6-amino-3-iodo-5-hydropyrazolo[3,4-d]pyrimidin-4-one(17)

A suspension of (16) (16.84 g, 41.36 mmol) in 1.5 L of 1 N sodiumhydroxide solution was heated to reflux. The mixture turned into ahomogenous solution and was cooled to 25° C. using an ice-water bath.Acetic acid (90 mL) was added and the solution was stored at 5° C.overnight. The crystals that formed were filtered, rinsed with ice-coldwater and dried: 7.47 g yield of 4. The filtrate was evaporated to avolume of about 500 mL and stored at 5° C. overnight. A second crop ofcrystals was collected (3.75 g). The filtrate was evaporated to about200 mL. The sodium acetate that formed was filtered off and the filtratewas stored at 5° C. overnight. Another crop of crystal was collected(2.25 g). Total yield: 13.47 g (83%); TLC (5:3:2, n-butanol/water/aceticacid), R_(f)=0.74; ¹H NMR (DMSO-d₆) δ 6.22 (1H, t, J=6.3 Hz, 1′—H), 4.33(1H, m, 3′-H), 3.73 (1H, m, 4′-H), 3.47 and 3.36 (2H, 2×m, 5′-Hs), 2.63and 2.12 (2H, 2×m, 2′-Hs). Anal. Calcd. For C₁₀H₁₂IN₅O₄ ^(·)0.7 H₂O; C,29.60; H, 3.33; N, 17.26. Found: C, 29.81; H, 3.02; N, 17.00.

N-(3-{1-[(2R,5R)-4-(hydroxymethyl)oxalan-2-yl]-6-amino-4-oxo(5-hydropyrazolo[3,4-d]pyrimidin-3-yl)}prop-2-ynyl)-2,2,2-trifluoroacetamide(18)

To a mixture of 17 (6.00 g, 15.26 mmol), CuI (297 mg, 1.56 mmol) andtetrakis[triphenylphosphine]palladium[0] in 30 mL of anhydrous DMF wasadded anhydrous triethylamine (3.14 mL) followed by propargyltrifluoroacetimide (4.29 g, 28.41 mmol). The reaction solution wasstirred under argon for 40 h. The DMF was evaporated off and theresidual oil was triturated in chloroform. The solid of crude 5 thatformed was filtered, rinsed with chloroform and dried. The solid wasdissolved in a minimum volume of DMF, absorbed onto silica gel andevaporated. The dry mixture was loaded onto a silica gel column andeluted with 10% methanol in ethyl acetate. The product fractions werepooled and evaporated. The residue was precipitated from ethylacetate/ether: 4.0 g (63%) yield; TLC (20% methanol in ethyl acetate),R_(f)=0.59; ¹H NMR (DMSO-d₆) δ 10.79 (1H, s, N₅—H), 10.16 (1H, t, J=5.2Hz, trifluoroacetimido N—H), 6.77 (2H, br s, 6-amino), 6.28 (1H, t,J=6.3 Hz, 1′—H), 5.23 (1H, d, J=4.1 Hz, 3′—OH), 4.72 (1H, t, J=5.1 Hz,5′-OH), 4.32 (3H, m, —CONH—CH₂— and 3′-H), 3.75 (1H, m, 4′-H), 3.50-3.29(2H, 2×m, 5′-Hs), 2.65 and 2.15 (2H, 2×m, 2′-Hs). Anal. Calcd. ForC₁₅H₁₅F₃N₆O₅.0.74H₂O; C, 41.93; H, 3.87; N, 19.56. Found: C, 42.33; H,3.64; N, 19.13.

N-(3-{1-[(2R,5R)-4-(hydroxymethyl)oxalan-2-yl]-6-amino-4-oxo(5-hydropyrazolo[pyriminin-3-yl)}propyl)-2,2,2-trifluoroacetamide(19)

To a solution of (18) (1.0 g, 2.40 mmol) in 100 mL of methanol,containing 0.12 g of 20% palladium hydroxide (preactivated with formicacid), was added 2.0 mL of 4 M triethylammonium formate buffer (pH 6.5).The mixture was shaken under 35 psi of hydrogen gas for 18 h (duringsome runs it was necessary to add additional catalyst for completereduction). The mixture was filtered through Celite and the filtrate wasevaporated. The residual oil was crystallized from water: 0.79 g (78%)yield; TLC (20% methanol in ethyl acetate), R_(f)=0.52; ¹H NMR (DMSO-d₆)δ 10.59 (1H, s, N₅—H), 9.47 (1H, br t, trifluoroacetimido N—H), 6.64(2H, br s, 6-amino), 6.27 (1H, t, J=6.3 Hz, 1′—H), 5.18 (1H, d J=4.4 Hz,3′—OH), 4.75 (1H, t, J=5.9 Hz, 5′—OH), 4.36 (1H, m, 3′-H), 3.48 and 3.61(2H, 2×m, 5′-Hs), 3.22, 2.68 and 1.87 (6H, 3×m, propyl methyleneprotons), 2.68 and 2.12 (2H, 2×m, 2′-Hs). Anal. Calcd. ForC₁₅H₁₉F₃N₆O₅.0.90H₂O; C, 41.27; H, 4.80; N, 19.25. Found: C, 41.57; H,4.50; N, 19.11.

N-(3-[(1E)-1-aza-2-(dimethylamino)prop-1-enyl]-[(2R,5R)-4-(hydroxymethyl)oxalan-2-yl]-6-amino-4-oxo(5-hydropyrazolo[5-4-d]pyriminin-3-yl)}propyl)-2,2,2-trifluoroacetamide(20)

To a solution of (19) (0.80 g, 1.98 mmol) in 5.0 mL of anhydrous DMF wasadded N,N-dimethylformamide dimethylacetal (3.1 mL). The solution wasstirred for 2.0 h. under argon and then evaporated. The residue wasevaporated twice from xylenes and then placed under vacuum. Theamorphous solid (20) that formed was triturated with ether andcollected: 773-mg (82%) yield; TLC (20% methanol in ethyl acetate),R_(f)=0.47; ¹H NMR (DMSO-d₆) δ 11.22 (1H, br s, N₅—H), 9.47 (1H, t,J=5.5 Hz, trifluoroacetimido N—H), 8.67 (1H, s, N═CH—N), 6.42 (1H, t,J=6.5 Hz, 1′—H), 5.22 (1H, d, J=4.3 Hz, 3′—OH), 4.75 (1H, t, J=6.1 Hz,5′—OH), 4.40 (1H, m, 3′-H), 3.77 (1H, m, 4′-H), 3.50 and 3.38 (2H, 2×s,5′-Hs), 3.18 and 3.05 (6H, 2×s, N,N-dimethyl Hs), 3.22, 2.72 and 1.89(6H, 3×m, propyl methylene Hs), 2.72 and 2.15 (2H, 2×m, 2′-Hs). Anal.Calcd. For C₁₈H₂₄F₃N₇O₅ 0.40₂ O; C, 44.80; H, 5.18; N, 20.32. Found: C,45.02; H, 4.96; N, 19.94.

N-{3-[1-((2R,5R)-5-{[bis(4-methoxyphenyl)phenylmethoxy]methyl}-4-hydroxyoxolan-4-oxo(5-hydropyrazolo[3,4-d]pyrimidin-3-yl)]propyl}-2,2,2-trifluoroacetamide(21)

To a solution of (20) (723-mg, 1.52 mmol) in 9.0 mL of anhydrouspyridine was added 4,4′-dimethoxytrityl chloride (0.61 g, 1.80 mmol).The reaction solution was stirred for 3.0 h. under argon and then pouredinto 100 mL of 5% sodium bicarbonate solution. The aqueous solution wasextracted with ethyl acetate (2×200 mL) and the dried extracts (sodiumsulfate) were evaporated. The crude product was purified by silica gelchromatography eluting with a solvent gradient of 0-5% methanol in ethylacetate (2% triethylamine). The product fractions were evaporatedaffording 21 as an amorphous solid: 724-mg (61%) yield; TLC (5% methanolin ethyl acetate), R_(f)=0.39; ¹H NMR (DMSO-d₆) δ 11.27 (1H, s, N₅—H),9.43 (1H, t, J=5.3 Hz, trifluoroacetimido N—H), 8.71 (1H, s, N═CH—N),7.32, 7.17 and 6.76 (13H, 3×m, aromatic), 6.45 (1H, t, J=6.3 Hz, 1′—H),5.26 (1H, d, J=5.3 Hz, 3′-OH), 4.45 (1H, m, 3′-H), 3.90 (1H, m, 4′-H),3.70 (6H, s, OMe Hs), 3.18 and 3.05 (10H, 2×s, N,N-dimethyl, 5′-Hs andCONH—CH₂), 2.62 and 1.65 (4H, 2×m, methylene Hs), 2.62 and 2.20 (2H,2×m, 2′-Hs). Anal. Calcd. For C₃₉H₄₂F₃N₇O₇.0.30H₂O; C, 59.81 ; H, 5.48;N, 12.52. Found: C, 59.80; H, 5.39; N, 12.63.

N-{3-[]-((2R,5R)-5{[bis(4-methoxyphenyl)phenylmethoxy]methyl}-4-{([bis(methylethyl)amino](2-cyanoethoxy)phosphinooxy}oxolan-2-yl)-6-amino-4-oxo(5-hydropyrazolo[3,4-d]pyrimidin-3-yl)]propyl}-2,2,2-trifluoroacetamide(22)

To a solution of (21) (700-mg, 0.900 mmol) in 22 mL of anhydrousmethylene chloride, containing 0.47 mL of diisopropylethylamine, wasadded 2-cyanoethyl N,N-diisopropylchlorophosphoramidite (0.34 mL, 1.52mmol). After stirring for 30 minutes under argon at 25° C. the solutionwas treated with 3.0 mL of methanol and diluted with 200 mL of ethylacetate. The solution was washed with 100 mL of 5% sodium bicarbonatesolution and dried over sodium sulfate and evaporated. The crude productwas purified by silica gel chromatography eluting with 2% triethylaminein ethyl acetate. The product fractions were evaporated and the residuewas precipitated from ether-hexane: 583-mg (66%) yield; TLC (ethylacetate), R_(f)=0.38; ³¹P NMR (DMSO-d₆, reference to 85% phosphoricacid) δ 145.50 and 144.72.

Example 4

This example illustrates the preparation of 3-{[5-(4,6-bis{(1E)-1-aza-2-[bis(2-methylpropyl)amino]vinyl}-3-ynylpyrazolo[3,4-d]pyrimidinyl)-2-{[bis(4-methoxyphenyl)phenylmethoxy]-methyloxolan-3-yloxy][ethyl(methylethyl)amino}-phosphino}propanenitrile (26)

5-(4,6-bis{(1E)-1-aza-2-[bis(2-methylpropyl)amino]vinyl}-3-prop-1-ynylpyrazolo[pyrimidinyl)-2(hydroxymethyl)oxolan-3-ol (24)

Compound (23) (1 mmol) can be stirred for 5 hr at room temperature with(dimethoxymethyl)bis(2-methylpropyl)amine (0.5 mL, 3.37 mmol). Thereaction mixture can be reduced in vacuo, and the protected compound canbe purified on silica gel to yield (24) (Vincent et al).

5-(4,6-bis{(1E)-1-aza-2-[bis(2-methylpropyl)amino]vinyl}-3-prop-1-ynylpyrazolo[pyrimidinyl)-2-{[bis(4-methoxyphenyl)phenylmethoxy]-methyl}oxolan-3-ol(25)

To a solution of (24) (1.50 mmol) in 9.0 mL of anhydrous pyridine4,4′-dimethoxytrityl chloride (0.61 g, 1.80 mmol) can be added. Thereaction solution can be stirred for 3.0 h. under argon and then can bepoured into 100 mL of 5% sodium bicarbonate solution. The aqueoussolution can be extracted with ethyl acetate (2×200 mL) and the extractscan be dried(sodium sulfate) and evaporated. The crude product can bepurified by silica gel chromatography with an appropriate gradient toyield (25).

3-{[5-(4,6-bis{(1E)-1-aza-2-[bis(2-methylpropyl)amino]vinyl}-3-prop-1-pyrimidinyl)-2-{[bis(4-methoxyphenyl)phenylmethoxy]methyl}-oxolan-3-yloxy][ethyl(methylethyl)amino}phosphino}propanenitrile(26)

To a solution of (25) (0.900 mmol) in 22 mL of anhydrous methylenechloride, containing 0.47 mL of diisopropylethylamine, 2-cyanoethylN,N-diisopropylchlorophosphoramidite (0.34 mL, 1.52 mmol) can be added.The solution can be stirred for 30 minutes under argon at 25° C. and thecan be treated with 3.0 mL of methanol and diluted with 200 mL of ethylacetate. The solution can then be washed with 100 mL of 5% sodiumbicarbonate solution and dried over sodium sulfate and evaporated. Thecrude product can be purified by silica gel chromatography with anappropriate gradient to yield (26).

Example 5

This example illustrates the synthesis of5-[4,6-diamino-3-(2-methoxyethynyl)pyrazolo[3,4-d]pyrimidinyl]-2-(hydroxymethyl)oxolan-3-ol(27)

5-[4,6-diamino-3-(2-methoxyethynyl)pyrazolo[3,4-d]pyrimidinyl]-2-(hydroxymethyl)oxolan-3-ol(27)

To a mixture of4,6-diamino-1-(2-deoxy-β-D-erythro-pentofuranosyl)-3-iodo-1H-pyrazolo[3,4-d]pyrimidine(4.2 g, 10.71 mmol), CuI (211 mg, 1.10 mmol), Pd(PPh₃)₄ (635 mg, 0.553mmol), and triethylamine (2.2 mL) in 20 mL of anhydrous DMF was addedmethyl propargyl ether (1.82 mL). The mixture was stirred under argonfor 16 h. and then evaporated to dryness. The residue was crystallizedfrom methanol: 3.20 g (89%) yield; TLC (30% methanol in ethyl acetate),R_(f)=0.63; ¹H NMR (DMSO-d₆) δ 7.44 (2H, br d, amino), 6.32 (1H, t,J=6.6 Hz, 1′—H), 6.33 (2H, br s, amino), 5.20 (1H, d, J=4.1 Hz, 3′-OH),4.75 (1H, br t, 5′—OH), 4.40 (2H, s, methylene), 4.36 (1H, m, 3′-H),3.76 (1H, m 4′-H), 3.47 & 3.32 (2H, 2×m, 5′-Hs), 3.32 (3H, s, methoxy),2.68 & 2.14 (2H, 2×m, 2′-Hs).

Synthesis of5-{6-[(1E)-1-aza-2-(dimethylamino)vinyl]-4-[(1Z)-1-aza-2-(dimethylamino)vinyl]pyrazolo[3,4-d]pyrimidinyl}-2-(hydroxymethyl)oxolan-3-ol,1-methoxyprop-1-yne (28)

Compound 27 (3.1 g, 9.28 mmol) was stirred in a solution of 30 mL ofN,N-dimethylformamide and 15 mL of N,N-dimethylformamide dimethyl acetalfor 14 h at 45° C. The solvents were evaporated and the residue wasevaporated twice from xylenes affording 28 as a foam which wasprecipitated from ethyl acetate-ether: 2.8 g (68%) yield; TLC (50%methanol in ethyl acetate), R_(f)=0.36.

Synthesis of3-[(5-{6-[(1E)-1-aza-2-(dimethylamino)vinyl]-4-[(1Z)-1-aza-2-(dimethylamino)vinyl]pyrazolo[3,4-d]pyrimidinyl}-2-{[bis(4-methoxyphenyl)phenyl-methoxy]methyl}oxolan-3-yloxy)[bis(methylethyl)amino]phosphinooxy]propanenitrile(29)

To a solution of 28 (2.7 g, 6.08 mmol) in 45 mL of anhydrous pyridinewas added dimethoxytrityl chloride (2.4 g). The resulting solution wasstirred for 3 h. at room temperature and then poured into 200 mL of 5%sodium bicarbonate solution. The mixture was extracted with ethylacetate and the extract was dried over sodium sulfate, filtered andevaporated. The residue was purified by silica gel chromatographyeluting with a gradient of 0-40% methanol in ethyl acetate. The pure5′-O-DMT derivative fractions were pooled and evaporated affording afoam: 1.0 g (22%) yield.

To a solution of DMT derivative (0.98 g, 1.31 mmol) in 16 mL ofanhydrous methylene chloride, containing 0.70 mL ofN,N-diisopropylethylamine was added 2-cyanoethyldiisopropylchlorophosphoramidite (0.50 mL) under argon. The solution wasstirred for 30 min at room temperature and then treated with 1.0 mL ofmethanol. The solution was loaded directly on to a silica gel column andeluted with a gradient of 0-20% methanol in ethyl acetate (2%triethylamine). The pure fractions were pooled and evaporated affordinga foam: 0.25 g (20%) yield.

Example 6

This example illustrates the preparation of3-[(5-{4-[(1Z)-1-aza-2-(methylamino)vinyl]-3-(2-furyl)pyrazolo[3,4-d]pyrimidinyl}-2-{[bis(4-methoxyphenyl)phenylmethoxy]methyl}oxolan-3-yloxy)[bis(methylethyl)amino]-phosphinooxy]propanenitrile (35) (See ReactionScheme 8)

(2-Furylmethoxymethylene)methane-1,1-dicarbonitrile (30)

To an ice-cold solution containing anhydrous methylene chloride (500mL), triethylamine (100 mL), and malonitrile (30 g, 454 mmol) was added2-furanyl chloride (50 g, 383 mmol) by dropwise addition over a 20 minperiod. Stirring was then continued for an additional hour at ambienttemperature. The reaction solution was washed with 1.5 L of ice-cold 2NHCl solution and then with 1.5 L of water. The organic phase wasevaporated affording an oil.

A portion of the product oil (4.6 g, 28.75 mmol) was dissolved in asolution consisting of 40 mL of dioxane and 4.0 mL of water. Dimethylsulfate (15 mL) and sodium bicarbonate (15 g) were added and thereaction solution was stirred for 2.5 h at 80° C. The mixture was thendissolved in 100 mL of water and the product was extracted with 200 mLof ethyl acetate. The organic solution was washed with 100 mL of 5%sodium bicarbonate solution followed by 100 mL of water. The solutionwas dried over sodium sulfate, filtered and evaporated affording an oilwhich solidified under vacuum: 2.72 g yield; TLC (1:1, ethylacetate/hexane), R_(f)=0.42; ¹H NMR ((DMSO-d₆) δ 8.25 (1H, m, aromatic),7.63 (1H, m, aromatic), 6.92 (1H, m, aromatic), 4.23 (3H, s, methoxy).

2-Amino-4-(2-furyl)furan-3-carbonitrile (31)

Hydrazine monohydrate (3.4 mL, 80 mmol) was added dropwise to anice-cold solution of 30 (2.72 g, 15.63 mmol) in 75 mL of methanol over aperiod of 15 min. The solution was then evaporated to dryness affordingan oil which solidified under vacuum. The solid was triturated in ether,filtered and dried: 2.2 g (81%) yield; TLC (ethyl actate), R_(f)=0.81;¹H NMR (DMSO-d₆) δ 7.77 (1H, s, furanyl), 6.80 (1H, m, furanyl), 6.61(1H, m, furanyl), 6.41 (2H, br s, amine).

3-(2-furyl)pyrazolo[3,4-d]pyrimidine-4-ylamine (32)

Compound 31 (25.7 g, 148 mmol) was stirred in 250 mL of formamide at190° C. for 4 h. The solution was then cooled to room temperature,diluted with 1.2 L of water and chilled in an ice-bath. The solid thatformed was filtered and dried: 22 g (74%) yield; TLC (5% methanol inethyl actate), R_(f)=0.25.

[5-(4-Amino-3-(2-furyl)pyrazolo[3,4-d]pyrimidinyl)-3-(4-methylphenylcarbonyloxy)-2-oxoetoxolan-2-yl]methyl 4-methylbenzoate (33).

Compound 32 (10 g, 49.7 mmol) was stirred in 200 mL of 0.29 M methanolicKOH solution for 5 min. The mixture was evaporated to dryness and theresidue was then dissolved in 40 mL of hot anhydrous DMF. The solutionwas cooled to room temperature and then diluted with 230 mL of anhydrousacetonitrile. The chlorosugar derivative (23 g, 59.14 mmol) was addedimmediately and the mixture was stirred for 45 min and then evaporatedto dryness. The residue was dissolved in 800 mL of ethyl acetate andwashed with water (2×800 mL). The organic solution was dried over sodiumsulfate, filtered and evaporated. The crude product was purified bysilica gel chromatography eluting with a gradient of 30-0% hexane inethyl acetate. The pure product fractions were evaporated and theresidue was crystallized from hot methanol: 3.4 g (12%) yield; TLC(ethyl actate), Rr=0.47; ¹H NMR ((DMSO-d₆) δ 8.27 (1H, s, 6-H), 7.96(1H, m, furanyl), 7.95, 7.84, 7.36 & 7.23 (8H, 4×d, toluoyl aromatic),6.83 (1H, m, furanyl), 6.80 (1H, t, J=6.3 Hz, 1′-H), 6.70 (1H, m,furanyl), 5.86 (1H, m, 3′-H), 4.64-4.42 (3H, m, 4′-H and 5′-Hs), 3.28 &2.76 (2H, 2×m, 2′-Hs), 2.39 & 2.36 (6H, 2×s, toluoyl methyls).

5-{4-[(1Z)-1-aza-2-(dimethylamino)vinyl]-3-(2-furyl)pyrazolo[3,4-d]pyrimidinyl}-2-3-ol(34)

A suspension of 33 (3.36 g, 6.08 mmol) in 17 mL of 0.12 M methanolicsodium methoxide solution was refluxed for 30 min. The resultingsolution was cooled to room temperature and neutralized by addition of0.12 mL of acetic acid. The solution was evaporated to dryness and theproduct was precipitated from methanol-ether and then recrystallizedfrom boiling water: 1.63 g (85%) yield of the deprotected nucleoside.

All of the nucleoside product from above was stirred in a solutionconsisting of 30 mL of anhydrous DMF and 15 mL of N,N-dimethylformamidedimethylacetal for 5 h. The solution was evaporated to dryness and theresidue was then evaporated twice from xylenes affording a foam: 1.89 g(99%) yield; TLC (20% methanol in ethyl actate), R_(f)=0.45; ¹H NMR((DMSO-d₆) δ 8.98 & 8.46 (2H, 2×s, formamidine C—H and 6-H), 7.97 (1H,m, furanyl), 7.81 (1H, m, furanyl), 6.65 (2H, m, 1′—H and furanyl), 5.30(1H, d, J=4.5 Hz, 3′—OH), 4.79 (1H, t, J=5.5 Hz, 5′—OH), 4.51 (1H, m,3′-H), 3.85 (1H, m, 4′-H), 3.57 & 3.40 (2H, 2×m, 5′-Hs), 3.26 & 3.21(6H, 2×s, N-Me protons), 2.88 & 2.30 (2H, 2×m, 2′-Hs).

3-[(5-{4-[(1Z)-1-aza-2-(methylamino)vinyl]-3-(2-furyl)pyrazolo[3,4-d]pyr{[bis(4-methoxyphenyl)phenylmethoxy]methyl}oxolan-3-yloxy)[bis(methylethyl)amino]-phosphinooxy]propanenitrile(35)

Dimethoxytrityl chloride (2.01 g) was added to a solution of 34 (1.84 g,4.95 mmol) dissolved in 30 mL of dry pyridine. The reaction solution wasstirred for 3 h at room temperature and then poured into 200 mL of 5%sodium bicarbonate solution. The product was extracted with 300 mL ofethyl acetate and the organic phase was dried over sodium sulfate andevaporated. The residue was purified using silica gel chromatographyeluting with a gradient of 0-5% methanol in ethyl acetate. The pureproduct fractions were evaporated affording a foam: 2.26 g (68%) yieldof the 5′-O-DMT derivative.

To a solution of the DMT derivative (2.18 g, 3.23 mmol) dissolved in 40mL of dry methylene chloride, containing 1.75 mL ofN,N-diisopropylethylamine, was added 1.25 mL of 2-cyanoethyldiisopropylchlorophosphoramidite. The solution was stirred under argonfor 15 min at room temperature and then treated with 5 mL of methanol.The resulting solution was diluted with 500 mL of ethyl acetate andwashed with 400 mL of 5% sodium bicarbonate solution. The organicsolution was dried over sodium sulfate, filtered and evaporated. Theresidue was purified by silica gel chromatography eluting with agradient of 5-10% methanol in ethyl acetate (2% triethylamine). The pureproduct fractions were evaporated affording a foam: 1.62 g (57%) yield;³¹P NMR (DMSO-d₆) δ 147.81 and 147.16.

Example 7

This example illustrates the preparation of3-[(5-{6-[(1E)-1-aza-2-(dimethylamino)vinyl]-4-[(1Z)-1-aza-2-(dimethylamino)vinyl]-3-(2-furyl)pyrazolo[3,4-d]pyrimidinyl}-2-{[bis(4-methoxyphenyl)phenylmethoxy]methyl}oxolan-3-yloxy)[bis(methylethyl)amino]phosphinooxy]propanenitrile(39, See Reaction Scheme 9)

3-(2-furyl)pyrazolo[3,4-d]pyrimidine-4,6-diamine (36)

A mixture of finely ground 31 (10.0 g, 57.47 mmol) and guanidinecarbonate (16.6 g, 91.95 mmol) was heated at 230° C. for 45 min. Themixture was cooled to room temperature and the solid was triturated in100 mL of boiling water. The solid (pure 36) was filtered, rinsed withwater and dried: 11.1 g (89%) yield; TLC (40% methanol in ethyl actate),R_(f)=0.66; ¹H NMR ((DMSO-d₆) δ 12.68 (1H, br s, N—H), 7.86 (1H, m,furanyl), 6.93 (2H, br s, —NH₂), 6.85 (1H, d, J=3.5 Hz, furanyl), 6.65(1H, m, furanyl), 6.10 (2H, br, s, —NH₂).

5-(4,6-diamino-3-(2-furyl)pyrazolo[3,4-d]pyrimidinyl)-2-(hydroxymethyl)oxolan-3-ol(37)

Compound 36 (10.5 g, 48.61 mmol) was stirred in 200 mL of 0.29 Mmethanolic KOH solution for 5 min. The mixture was evaporated to drynessand the residue was then dissolved in 105 mL of hot anhydrous DMF. Thesolution was cooled to room temperature and then diluted with 620 mL ofanhydrous acetonitrile. The chlorosugar derivative (23 g, 59.14 mmol)was added immediately and the mixture was stirred for 40 min and thenfiltered. The filtrate was evaporated to dryness and the residue waschromatographed through a silica gel column eluting with ethyl acetate.The nucleoside fractions were evaporated affording 2.8 g (10% yield) ofthe toluoyl protected nucleoside as a mixture of alpha- andbeta-anomers. This mixture was refluxed in 40 mL of 0.19 M methanolicsodium methoxide for 45 min. The reaction solution was placed in afreezer overnight producing a crop of crystals corresponding to the purebeta-anomer 37: 690 mg yield; TLC (20% methanol in ethyl actate),R_(f)=0.32; ¹H NMR (DMSO-d₆) δ 7.90 (1H, m, furanyl), 6.99 (2H, br s,amino), 6.86 (1H, d, J=4.1 Hz, furanyl), 6.68 (1H, m, furanyl), 6.41(1H, t, J=6.6 Hz, 1′—H), 6.26 (2H, br s, amino), 5.21 (1H, d, J=4.4 Hz,3′—OH), 4.82 (1H, t, J=5.8 Hz, 5′—OH), 4.42 (1H, m, 3′-H), 3.79 (1H, m,4′-H), 3.52 & 3.41 (2H, 2×m, 5′-Hs), 2.75 & 2.18 (2H, 2×m, 2′-Hs).

5-{6-[(1E)-1-aza-2-(dimethylamino)vinyl]-4-[(1Z)-1-aza-2-(dimethylamino)vinyl]-3-(2-furyl)pyrazolo[3,4-d]pyrimidinyl}-2-(hydroxymethyl)oxolan-3-ol(38)

A solution of 37 (0.68 g, 2.05 mmol) in 30 mL of anhydrous DMF and 15 mLof N,N-dimethylformamide dimethylacetal was stirred at room temperaturefor 24 h. The solution was evaporated to dryness and the residue wasevaporated twice from xylenes affording a foam: 0.90 g (99%) yield; TLC(50% methanol in ethyl actate), R_(f)=0.38; ¹H NMR (DMSO-d₆) δ 8.93 &8.77 (2H, 2×s, formamidine C-Hs), 7.94 (1H, m, furanyl), 7.76 (1H, m,furanyl), 6.62 (1H, m, furanyl), 6.60 (1H, t, J=6.6 Hz, 1′—H), 5.25 (1H,d, J=4.4 Hz, 3′—OH), 4.84 (1H, t, J=5.9 Hz, 5′—OH), 4.47 (1H, m, 3′-H),3.83 (1H, m, 4′-H), 3.56 & 3.41 (2H, 2×m, 5′-Hs), 3.25, 3.18, 3.16 &3.03 (12H, 4×s, N-methyls), 2.82 & 2.22 (2H, 2×m, 2′-Hs).]

3-[(5-{6-[(1E)-1-aza-2-(dimethylamino)vinyl]-4-[(]Z)-1-aza-2-(dimethylamino)vinyl]-3-(2-furyl)pyrazolo]3,4-d]pyrimidinyl}-2-{[bis(4-methoxyphenyl)phenylmethoxy]methyl}oxolan-3-yloxy)[bis(methylethyl)amino]phosphinooxy]propanenitrile(39)

Dimethoxytrityl chloride (0.85 g) was added to a solution of 38 (0.90 g,2.04 mmol) in 12 mL of dry pyridine. The reaction solution was stirredfor 2 h at room temperature and then poured into 200 mL of 5% sodiumbicarbonate solution. The product was extracted with ethyl acetate(3×300 mL) and the pooled organic extracts were dried over sodiumsulfate and evaporated. The residue was purified using silica gelchromatography eluting with a gradient of 20-30% methanol in ethylacetate. The pure product fractions were evaporated affording a foam:286-mg yield of the 5′-O-DMT derivative.

To a solution of the DMT derivative (286 mg, 0.384 mmol) dissolved in 5mL of dry methylene chloride, containing 0.23 mL ofN,N-diisopropylethylamine, was added 0.17 mL of 2-cyanoethyldiisopropylchlorophosphoramidite. The solution was stirred under argonfor 15 min at room temperature and then treated with 0.5 mL of methanol.The resulting solution was diluted with 100 mL of ethyl acetate andwashed with 75 mL of 5% sodium bicarbonate solution. The organicsolution was dried over sodium sulfate, filtered and evaporated. Theresidue was purified by silica gel chromatography eluting with agradient of 0-30% methanol in ethyl acetate (2% triethylamine). The pureproduct fractions were evaporated affording a foam: 230 mg (12%) yield;³¹P NMR (DMSO-d₆) δ 147.77 and 147.08.

Example 8

This example illustrates the preparation of4-[1-(5-{[bis(4-methoxyphenyl)phenylmethoxy]methyl}-4-{[bis(methylethyl)amino](2-cyanoethoxy)phosphinooxy}oxolan-2-yl)-2,4-dioxo-1,3-dihydropyrimidin-5-yl]but-3-ynyl4-methylbenzoate (see, 42 Reaction Scheme 10)

Synthesis of 3-Butyn-1-yl p-Toluate (40)

In a 500 mL round bottom flask equipped with a magnetic stirring bar andunder inert atmosphere, 3-butyn-1-ol (50.3 g, 0.718 mol) was dissolvedwith anhydrous pyridine (200 mL) and the solution was cooled in an icewater bath. To the cold solution, using an addition funnel, p-toluylchloride (136.6 g, 0.86 mol, 1.2 eq) was added dropwise and the reactionmixture was stirred at room temperature overnight.

To the mixture were added diethyl ether (350 mL) and water (100 mL). Theorganic layer was separated, and the aqueous solution was washed withdiethyl ether (150 mL). The organic fractions were combined and washedwith 10% HCl (3×100 mL), saturated NaHCO₃ solution (2×100 mL) and water(1×50 mL). The resulting solution was dried over anhydrous Na₂SO₄,filtered and the solvent was removed to give 142 g (quantitative yield)of (40) as an off-white solid. The product can be recrystallized formhexane or methanol, but was sufficiently pure to proceed to the nextstep.

¹H NMR (CDCl₃, 300 MHz) δ (ppm) 7.95 (d, 2H, J=8.1 Hz), 7.24 (d, 2H,J=8.1 Hz), 4.41 (t, 2H, J=6.8 Hz), 2.67 (dd, 2H, J=2.6 J₂=6.8 Hz), 2.40(s, 3H), 2.03 (t, 1H, J=2.4 Hz).

5′-DMT-5-[4-(p-toluyloxy)butynyl]-2′-deoxyurdine (41)

A mixture of 5-iodo-2′-deoxyuridine (4.0 g, 11.30 mmol),4-(p-toluyloxy)butyne (40) (5.7 g, 30.3 mmol), CuI (222 mg, 1.16 mmol),tetrakis[triphenylphosphine]palladium[0] (0.67 g, 0.583 mmol) andtriethylamine (2.0 mL) was stirred in 30 mL of anhydrous DMF under argonfor 16 h. The mixture was evaporated to dryness and the residual oilsolidified after stirring in 100 mL of ether. This solid was filteredand dried under vacuum.

A portion of the crude product (1.5 g) was dissolved in 20 mL ofanhyrdrous pyridine and treated with dimethoxytrityl chloride (1.3 g).The solution was stirred for 2.0 h. under argon and then poured into 150mL of 5% sodium bicarbonate solution. The product was extracted with 200mL of ethyl acetate. The extract was dried over sodium sulfate, filteredand the solvent evaporated. The residue was purified by silica gelchromatography eluting with a gradient of 30-0% hexane in ethylacetate). The product fractions were evaporated, affording a foam:957-mg yield. TLC (30% hexane in ethyl acetate), R_(f)=0.37; ¹H NMR(DMSO-d₆) δ 11.66 (1H, s, N—H), 7.9-6.8 (18H, aromatic protons), 6.11(1H, t, J=6.6 Hz, 1′—H), 5.35 (1H, br s, 3′—OH), 4.29 (1H, m, 3′-H),4.15 (2H, t, J=6.8 Hz, butyne methylene), 3.92 (1H, m, 4′-H), 3.71 (6H,s, methoxy groups), 3.24 & 3.07 (2H, 2×m, 5′-Hs), 2.64 (2H, t, J=6.8 Hz,butyne methylene), 2.37 (3H, s, toluyl methyl), 2.23 (2H, m, 2′-Hs).

4-[1-(5-{[bis(4-methoxyphenyl)phenylmethoxy]methyl}-4-{[bis(methylethyl)amino](2-cyanoethoxy)phosphinooxy}oxolan-2-yl)-2,4-dioxo-1,3-dihydropyrimidin-5-yl]but-3-ynyl4-methylbenzoate (42)

To a solution of the DMT derivative from above (0.92 g, 1.28 mmol) in 15mL of anhydrous methylene chloride, containing 0.75 mL ofN,N-diisopropylethylamine, was added 2-cyanoethyldiisopropylchlorophosphoramidite (0.56 mL). The solution was stirred for30 min at room temperature under argon and then treated with 1.0 mL ofmethanol. The solution was evaporated down to about a 5 mL volume andloaded directly on to a silica gel column and eluted with 40% hexane inethyl acetate (2% triethylamine). The pure fractions were pooled andevaporated, affording a foam: 0.91 g of (42) (78%) yield; ³¹P NMR(DMSO-d₆) δ 147.72 & 147.39.

Example 9

This example illustrates the enhanced ability of modifiedoligonucleotides to discriminate between related target sequences.

In this example, modified oligonucleotides were prepared containingPPPA, PPG and a minor groove binder. As FIG. 3 illustrates, the use of aMGB in combination with PPPA and PPG increases the T_(m) and allows thedesign of shorter probes compatible with PCR extension temperatures.These modified oligonucleotides also yield increased mismatchdiscrimination. In a first design of a 18-mer fluorescein-ODN-Red13quencher-MGB real-time PCR probe, poor discrimination of an A/Tmismatch was observed as shown in FIG. 3A. Re-design of the probeagainst the opposite strand, putting the mismatch under the MGB andsubstituting PPPA for A and PPG for G as indicated, allows shortening ofthe probe to a 15-mer. This probe now gives good mismatch discriminationas shown in FIG. 3B.

A thermodynamic investigation of mismatch discrimination was performedon a set of oligonucleotides hybridized to a set of targets perfectlymatch or containing a single mismatch. The target sequences contain a)normal As, b) PPPA, c) normal As and a 3′-MGB and d) PPPA and a 3′-MGB,respectively. The sequences for the probes and targets are shown belowin Table 3a and 3b. The determination of T_(m)s and the calculation of

TABLE 3a and 3b Probe and target sequences Num- SEQ ID ber MismatchProbe Sequence NO: A. Probe Sequences - Mismatch Underlined 1 ComplementAAAGTTATGTCTACTTACAGAAA 17 2 A/C AAAGCTATGTCTACTTACAGAAA 18 3 A/CAAAGTCATGTCTACTTACAGAAA 19 4 T/G AAAGTTGTGTCTACTTACAGAAA 20 5 A/CAAAGTTACGTCTACTTACAGAAA 21 6 C/A AAAGTTATATCTACTTACAGAAA 22 7 A/CAAAGTTATGCCTACTTACAGAAA 23 8 G/T AAAGTTATGTTTACTTACAGAAA 24 9 A/CAAAGTTATGTCCACTTACAGAAA 25 10  T/G AAAGTTATGTCTGCTTACAGAAA 26 11  G/TAAAGTTATGTCTATTTACAGAAA 27 12  A/C AAAGTTATGTCTACCTACAGAAA 28 13  A/CAAAGTTATGTCTACTCACAGAAA 29 14  T/G AAAGTTATGTCTACTTGCAGAAA 30 B. TargetSequences - A′ = PPPA 1     GTAAGTAGACATAAC 31 2  GTA′A′GTA′GA′CA′TA′A′C 32 3   GTAAGTAGACATAAC-MGB 33 4GTA′A′GTA′GA′CA′TA′A′C-MGB 34

TABLE 3c Thermodynamic comparison of mismatch discrimination in terms offree energy increment at 50° C. where ΔΔG°₅₀ = R°ln(K_(match)/K_(mismatch)) Number Mismatch A PPPA MGB MGB + PPPA 2 A/C2340 2930 2870 5320 3 A/C 2560 3280 4100 6320 4 T/G 1950 1810 4200 59005 A/C 3520 3760 3830 4980 6 C/A 5030 5340 4190 5970 7 A/C 3000 3370 43105260 8 G/T 3040 3260 3070 4820 9 A/C 3290 3440 3810 5630 10 T/G 18001950 2090 3350 11 G/T 3340 3120 3630 5070 12 A/C 2940 3620 2550 4490 13A/C 2360 3210 1820 3980 14 T/G 1600 2010 2000 2480

ΔΔG^(o) ₅₀ is described in Example 9. Table 3c clearly shows increasedmismatch discrimination when PPPA is substituted for A and even largerdiscrimination when PPPA is combined with a MGB.

Comparison of the thermodynamic discrimination of mismatched base pairsformed in MGB-ODNs containing HO—PPPA/HO—PU with PPPA/PU at 37° C. isshown in Table 4. The ODNs containing the modified bases in combinationwith MGB were hybridized to their complements. Mismatches are underlinedin the sequences shown in Table 4. As shown in this table, HO—PPPA andHO—PU substitution compared to PPPA and PU, shown for the most partincreased mismatch discrimination.

TABLE 4 Comparison of thermodynamic discrimination of mismatched basepairs formed by HOPPPA or HOPU vs PPPA and PU in the 8-mer duplexes(+MGB). PPPA/ HOPPPA/ PPPA/ HOPPPA/ SEQ PU HOPU SEQ PU HOPU Sequence ofID ΔΔG ΔΔG Sequence of ID ΔΔG ΔΔG Duplex NO: caL/mol cal/mol Duplex NO:cal/mol cal/mol Match CGUCACUG-MGB 35 Match UAUUAUUG-MGB 45 AGCTGTGACTAATAATAACC 1 CGUCACUG-MGB 36 4250 4350 10 UAUUAUUG-MGB 46 4400 5000AGCTGTGACT AATTATAACC 2 CGUCACUG-MGB 37 3450 3540 11 UAUUAUUG-MGB 473740 3760 AGCGGTGACT AATGATAACC 3 CGUCACUG-MGB 38 4860 4530 12UAUUAUUG-MGB 48 6630 6840 AGCCGTGACT AATCATAACC 4 CGUCACUG-MGB 39 48704850 13 UAUUAUUG-MGB 49 5090 5730 AGCAGAGACT AATAAAAACC 5 CGUCACUG-MGB40 4190 4360 14 UAUUAUUG-MGB 50 5920 6520 AGCAGGGACT AATAAGAACC 6CGUCACUG-MGB 41 3930 3940 15 UAUUAUUG-MGB 51 4120 4530 AGCAGCGACTAATAACAACC 7 CGUCACUG-MGB 42 2600 2300 AGCAATGACT 8 CGUCACUG-MGB 43 43604210 AGCATTGACT 9 CGUCACUG-MGB 44 4420 4610 AGCACTGACT ΔΔG wascalculated at 37° C.

Example 10

This example illustrates the UV melting studies carried out usingoligonucleotides of the present invention.

Hybrids formed between unmodified ODNs or MGB-probes and theircomplements were melted at a rate of 0.5° C./min, on a Lambda 2S(Perkin-Elmer) spectrophotometer with a PTP-6 automatic multicelltemperature programmer. T_(m) data was prepared using 0.5× SSPE buffer(Sigma, pH 7.4). Each ODN (1 μM of each strand) was mixed with itscomplement to give a 1:1 ratio. Prior to melting, samples were denaturedat 100° C. and then cooled to 10° C. over a 10 min period. Mismatchdiscrimination for each type of duplex was calculated in terms of ΔΔG at50° C. using the equation:ΔΔG ^(o) ₅₀ =R ^(o) in(K _(match) /K _(mismatch)).

The term K_(match)/K_(mismatch) can be determined using the relativefractions of duplex and single strands calculated from the meltingcurves at 50° C. (see Lohkov, S. G. & Pyshnyi, FEBS Letters 420:134-138(1997)).

Example 11

This example illustrates the hybridization of DNA to oligonucleotideglass microarrays prepared as described in co-pending application Ser.No. 09/364,320 and further optimized for 8-10 mer MGB probes.

DNA (oligonucleotide or PCR amplicon) at 1-5×10⁻⁷ M in 5×SSPE, 0.1%Trition X-100, 10% formamide was hybridized to the microarray inFrame-Seal Chambers (MJ Research) under the following conditions: 5minutes at 55° C., slow cooling at 0.1° C./sec to 35° C., 60 minutes at55° C. The slides were then washed in 0.5×SSPE for 5 minutes at 45° C.Slides were dried under a stream of air and scanned using an Array WorksFluorescent scanner (Applied Precision). The washing procedure can berepeated under more stringent conditions if required.

Example 12

This example illustrates a single base primer extension assay.

Single stranded template DNA and 6-mer primer (20 μM each), 1× Thermopolbuffer (New England Biolabs), 10 mM manganese chloride (USB), werecombined and incubated 5 minutes at 50° C. Then 5 μCi α³²P ddATP and 8units Bst polymerase (NEB) were added, bringing total volume to 10 μl,and incubated 15 minutes at 50° C. After incubation, 6 μl stop solution(95% formamide, 20 mM EDTA) was added and reactions were cooled to roomtemperature. Samples were diluted 1:10 in denaturing dye (35% formamide,0.05% xylene cyanol, 0.05% bromophenol blue, 1 mM EDTA), and aliquotswere analyzed by electrophoresis on a denaturing 10% polyacrylamide gel.

The use of modified bases in primer extension assays for SNP typing isillustrated in Table 5. Primer extension with Bst polymerase (NEB) wasevaluated with a primer substituted with different modified bases andthe amount of product was measured based on the incorporatedradioactivity using gel electrophoresis.

TABLE 5 Comparison of ³²P-incorporation in primer extension product bypolyacrylamide gel electrophoresis using AAC CAC TCT GTC CTA (SEQ IDNO:52) template Primer Relative Signal TGAGAC ++ U^(prop)GAGAC +U^(prop)G^(prop)AGAC +++ U^(prop)G^(prop)A^(prop)GAC +++++U^(prop)G^(prop)A^(prop)G^(prop)AC +++++U^(prop)G^(prop)A^(prop)G^(prop)A^(prop)C +U^(prop)G^(prop)A^(prop)G^(prop)A^(prop)C^(prop) 0.5+

Example 13

This example illustrates the use of the algorithm described in thespecification to predict the T_(m) of modified oligonucleotidescontaining PPG both with and without a minor groove binder (CDPI₃)

Using thermodynamic parameters in Tables 2a/2b and the correctionformula for the MGBs contribution, T_(m) of PPG oligonucleotides withand without a MGB can be calculated with algorithm procedures asdescribed above. The thermodynamic parameters of the nearest neighborpairs that are not G-containing do not change when the oligonucleotidesare substituted with PPG. Similarly the thermodynamic parameters of thenearest-neighbor pairs do not change when MGB containingoligonucleotides are substituted with PPG. Table 6 illustrates theability of the algorithm to predict the T_(m) of oligonucleotidescontaining PPG alone or in combination with a minor groove binder(CDPI₃). In Table 6, all Gs are substituted with PPGs.

TABLE 6 Comparison of experimental T_(m)s with that of predicted T_(m)susing the nearest-neighbor thermodynamic parameters for PPG containingoligonucleotides and PPG containing oligonucleotides attached to a MGBODN Duplex MGB-ODN Duplex SEQ Stability ° C. Stability ° C. 5′-ProbeSequence-3′ ID NO: Tm_(exp) Tm_(calc) Err Tm_(exp) Tm_(calc) ErrCTGTAAGTAGATATAAC 53 51.84 53.23 1.39 65.88 66.69 0.81 GGCAAGATATATAG 5450.21 49.81 −0.40 66.37 65.56 −0.81 GTGACGCAGATTCC 55 61.27 61.06 −0.2176.97 75.19 −1.78 GTAAGTAGACATAAC 56 52.12 51.78 −0.34 64.64 63.31 −1.33CAGGGAGCTTTGGA 57 59.9 60.22 0.32 74.39 71.47 −2.92 CACTCGTGAAGCTG 5860.85 59.49 −1.36 74.04 72.26 −1.78 GTAAGTAGGCATAAC 59 55.74 55.47 −0.2766.91 66.00 −0.91 CCGGATGTAGGATC 60 57.52 59.05 1.53 69.3 70.03 0.73GATTACCTGGATTT 61 50.64 50.32 −0.32 62.29 62.33 0.04 CCGTCAATGGTCAC 6258.66 60.01 1.35 70.13 69.91 −0.22 CAGCACGTAGCC 63 57.31 58.07 0.7669.29 67.60 −1.69 CGGCTACGTGCTGG 64 65.19 66.01 0.82 76.12 74.79 −1.33CGGCTACATGCTGG 65 61.14 61.95 0.81 71.56 72.99 1.43 CTAAATCTGCCG 66 50.448.09 −2.31 62.08 60.19 −1.89 TCTGGATGATGGGCA 67 61.74 61.95 0.21 71.6572.13 0.48 GTTCATGGGTGTAAT 68 57.51 57.77 0.26 66.94 68.79 1.85CGGAGGTAGGATCA 69 59.24 59.46 0.22 69.46 70.93 1.47 CCACCCGCCTCAG 7060.73 61.14 0.41 71.43 70.74 −0.69 CACAGGAGTGGTTGG 71 63.07 64.40 1.3372.28 72.92 0.64 CGGACCAGTGCGTG 72 68.1 67.58 −0.52 77.92 76.80 −1.12TCGGACCAGTGCGT 73 65.04 66.00 0.96 74.94 75.62 0.68 AACGGGGTACGATA 7457.93 57.11 −0.82 67.79 67.08 −0.71 CAGTTGAGATTCTAAGAC 75 60.06 60.150.09 67.15 67.43 0.28 AGGGGCGTCTTG 76 60.78 58.57 −2.21 71.62 72.76 1.14GTAAGTAGGCATAGC 77 58.34 58.95 0.61 65.95 66.99 1.04 TGCCCAGCCCCAG 7863.13 63.40 0.27 71.28 71.32 0.04 CCAACACTCGTGAA 79 54.87 56.14 1.2762.07 63.54 1.47 GTAAGTAGACACAGC 80 59.48 58.41 −1.07 65.79 66.27 0.48TCGGACCAGTGC 81 58.02 58.55 0.53 65.99 66.35 0.36 CGATCACGCTGGC 82 62.1262.75 0.63 69.18 71.81 2.63 GTCCTGGGGGTGG 83 65.19 64.54 −0.65 72.7872.53 −0.25 GTAAGTAGGTGTGAC 84 60.7 59.70 −1.00 66.92 67.00 0.08GGTTGTACGGGTTCACG 85 68.38 68.81 0.43 74.16 75.38 1.22 GGACCAGTGCGTGA 8666.84 65.46 −1.38 73.38 71.53 −1.85 GTAAGTAGACGCAGC 87 62.91 62.44 −0.4768 67.82 −0.18 GTAAGTAGGCGCAGC 88 65.52 65.91 0.39 69.8 70.34 0.54GTAAGTAGGCGCGGC 89 68.71 68.96 0.25 72.26 72.76 0.50 GGTTCCCGAGCG 9062.15 61.14 −1.01 65.75 64.22 −1.53

The accuracy of the prediction algorithm is about ±1 and ±2° C. for PPGcontaining oligonucleotides and PPG containing MGB-oligonucleotides,respectively. Accordingly, a sequence of interest can be obtained from asource such as Genbank, and a T_(m) window can then be set as arequirement for a set of probes or primers. Using the algorithm above,and information from the nearest-neighbor parameters, a collection ofprobe or primer sequences with the desired T_(m)s can be calculated.

Alternatively, the algorithm can be used to select nearest-neighborparameters from a selection of modified bases and to calculate thestability of more than one sequence of the same length to give the samepredetermined thermodynamic stability, with the selected modified bases.

Still further, the algorithm can be used to select one or more modifiedbases that allow the design of oligonucleotides of the same base pairlength and substantially the same stability (T_(m)). These modifiedbases can be selected from a database containing pre-determinedthermodynamic nearest neighbor parameters from an collection of modifiedpurines and/or modified pyrimidines. Preferably, the database containsnearest-neighbor parameters of 3-substituted pyrazolo[3,4-d]pyrimidinesand/or 5-substituted pyrimidines.

Example 14

This example illustrates the use of modified oligonucleotides in anInvader™ assay.

The cleavase-based assay is shown in FIG. 4 detects specific DNA and RNAsequences to cleave a complex formed by the hybridization of twooverlapping oligonucleotides to a target. The enzyme cleaves theoverhanging “flap”, which serves as an invader probe in the detectioncassette probe where cleavage releases a fluorescence signal. The firstcleavage takes places only when the single base mismatch in the invaderis a perfect match. No reaction takes place with a mismatch target B.The cleaved “flap” serves as an invader in the detection cassette,leading to the release of fluorescence in the second cleavage step.

Table 7a and 7b

Comparison of Cleavase-Bases Amplification System with DifferentModified Bases Substituted in the Genomic and Invader Probes

TABLE 7a Modified Bases # Probe¹ Substituted in Probe Sequence² Length 1Cassette None 41 2 Invader T None 59 3 Invader M1 Five A24 bases 32 4Genomic T None 43 5 Genomic M1 Six A14 bases 35 6 Genomic M2 Five A24bases 31 ¹Unmodified Probes and assay conditions are similar to thosedescribed by Hall et al, PNAS 97: 8272-77 (2000) ²A14 ishydroxypropynylPPA and A24 is 3-iododiaminoPPA

TABLE 7b Endpoint Match/Mismatch Genomic probe Signal Ratio ΔF RFU³ 4 54100 5 10 8000 6 7 11900 ³ΔF is end point fluorescence differencebetween match and mismatch in relative fluorescence units

Table 7a shows a comparison of the effect of different modified baseswhen substituted in the Invader and genomic probes. The traditionalinvaderT (2) was substituted with 3-iododiaminoPPPA to give invader M1which now has a length of 32 with a similar T_(m) as the 59-mer (2).Similarly the traditional genomic probe (4) was substituted3-hydroxypropynylPPPA and 3-iododiaminoPPPA to give (5) and (6)respectively. Both of these probes are substantially shorter than thetraditional (4). Using invaderM1 (3) in combination with the genomicprobes 4-6 individually results in (Table 7b) improved performance ofboth genomic probes containing the modified bases (5 and 6) compared tothe traditional genomic probe (4). As shown both the endpointmatch/mismatch signal ratios and the end point fluorescence showincreases compared to the unmodified genomic probe.

All publications and patent applications cited in this specification areherein incorporated by reference as if each individual publication orpatent application were specifically and individually indicated to beincorporated by reference. Although the foregoing invention has beendescribed in some detail by way of illustration and example for purposesof clarity of understanding, it will be readily apparent to those ofordinary skill in the art in light of the teachings of this inventionthat certain changes and modifications may be made thereto withoutdeparting from the spirit or scope of the appended claims.

1. A composition having a plurality of oligonucleotides, saidcomposition comprising: a first oligonucleotide with a first sequencehaving at least one modified base and a first T_(m); and a secondoligonucleotide with a second sequence and a second T_(m), wherein saidfirst T_(m) and said second T_(m) are level within about 5° C. of eachother.
 2. The composition of claim 1, wherein said first oligonucleotideis within about ±2 bases of said second oligonucleotide.
 3. Thecomposition of claim 1, wherein said at least one modified base in saidfirst sequence is a member selected from the group consisting of a baseattached to an amino acid, a locked-nucleic acid base and a universalbase.
 4. The composition of claim 1, wherein said at least one modifiedbase in said first sequence is selected from the group consisting of3-substituted pyrazolo[3,4-d]pryimidine and 5-substituted pyrimidine. 5.The composition of claim 1, wherein said at least one modified base insaid first sequence is a member selected from the group consisting ofPPA, PPG, PPPA, PPPG, PU, PC, HOPU, HOBuU, HOBuC, (NH₂)₂PPPA,(NH₂)₂PPPAOH, (NH₂)₂BuPPAOH, (NH₂)₂PPAI, and HOBuPPG.
 6. The compositionof claim 1, wherein said second sequence has at least one modified base.7. The composition of claim 6, wherein said at least one modified basein said second sequence is a member selected from the group consistingof a base attached to an amino acid, a locked-nucleic acid base and auniversal base.
 8. The composition of claim 6, wherein said at least onemodified base in said second sequence is a member selected from thegroup consisting of PPA, PPG, PPPA, PPPG, PU, PC, HOPU, HOBuU, HOBuC,(NH₂)₂PPPA, (NH₂)₂PPPAOH, (NH₂)₂BuPPAOH, (NH₂)₂PPAI, and HOBuPPG.
 9. Thecomposition of claim 1, wherein said first sequence has a MGB attachedthereto.
 10. The composition of claim 1, wherein said second sequencehas a MGB attached thereto.
 11. The composition of claim 1, wherein saidat least one modified base in said first sequence decreases stability ofsaid first oligonucleotide.
 12. The composition of claim 1, wherein saidat least one modified base in said first sequence increases stability ofsaid first oligonucleotide.
 13. The composition of claim 1, wherein saidfirst oligonucleotide and said second oligonucleotide are arrayed on asurface.
 14. The composition of claim 13, wherein said array comprises asolid support and a plurality of attached oligonucleotides, and whereinsaid plurality of oligonucleotides contain at least one modified baseselected from the group consisting of unsubstitutedpyrazolo[3,4-d]pyrimidines, 3-substituted pyrazolo[3,4-d]pyrimidines and5-substituted pyrimidines.
 15. The composition of claim 13, wherein saidarray comprises a solid support and a plurality of attachedoligonucleotides, and wherein said plurality of oligonucleotides containat least one modified base selected from each of the groups consistingof 3-substituted pyrazolo[3,4-d]pyrimidines and 5-substitutedpyrimidines.
 16. The composition of claim 13, wherein said arraycomprises from about 10 to about 10,000 attached oligonucleotides, eachhaving T_(m)s within about 2° C. of each other and basepair lengthswithin about 2 bases of each other.